Abstract: The MADS-box gene family is involved in many processes during plant growth and development, such as flowering time, floral organ differentiation, root growth, meristem differentiation, ovary and gamete development, fruit enlargement and senescence. In this study, we used rape (Brassica napus) genome sequencing data with bioinformatics methods to identify and annotate the MADS-box genes. Rape contains 307 members of MADS-box gene family. According to the evolutionary relationships, these genes can be divided into two subfamilies: I-type, also known as M-type, containing three subclades, α, β, and γ; II type, also known as MIKC-type containing two subclades, MIKCC and MIKC*. MIKCC can be further divided into 13 groups. The number of MADS-box genes is greater in the A than C subgenome chromosome of B. napus. For the gene structure, the sequence is longer for MIKC-type than M-type genes and contains more exons. The number of motifs in M-type genes is about 2-5, and MIKC-type genes contain an average of 7 motifs. Synteny analysis revealed that whole-genome duplication played a major role in the expansion of the BnaMADS gene family, especially the MIKC-type subfamily. The selection pressure of the MIKC-type subfamily was about 2 times that for the M-type, which resulted in the selective preservation of MIKC-type subfamily genes during evolution.
图2 甘蓝型油菜MADS-box基因在染色体上的分布 Figure 2 Chromosomal location of MADS-box genes in Brassica napus
图3https://www.chinbullbotany.com/article/2017/1674-3466/1674-3466-52-6-699/img_3.png<b>图3</b> 甘蓝型油菜MADS-box基因在染色体上分布的统计<br/><b>Figure 3</b> Statistics of MADS-box genes in chromosome of <i>Brassica napus</i> Figure 3https://www.chinbullbotany.com/article/2017/1674-3466/1674-3466-52-6-699/img_3.png<b>图3</b> 甘蓝型油菜MADS-box基因在染色体上分布的统计<br/><b>Figure 3</b> Statistics of MADS-box genes in chromosome of <i>Brassica napus</i>
AiroldiCA, DaviesB (2012). Gene duplication and the evolution of plant MADS-box transcription factors.J Genet Genomics 39, 157-165. DOI:10.1016/j.jgg.2012.02.008PMID:22546537URLSince the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a much wider range of species. Over the course of millions of years the number of MADS-box genes in plants has increased to the point that the Arabidopsis genome contains more than 100. The understanding gained from studying the evolution, regulation and function of multiple MADS-box genes in an increasing set of species, makes this large plant transcription factor gene family an ideal subject to study the processes that lead to an increase in gene number and the selective birth, death and repurposing of its component members. Here we will use examples taken from the MADS-box gene family to review what is known about the factors that influence the loss and retention of genes duplicated in different ways and examine the varied fates of the retained genes and their associated biological outcomes. [本文引用: 1]
Alvarez-BuyllaER, PelazS, LiljegrenSJ, GoldSE, Bur- geffC, DittaGS, de PouplanaLR, Martínez-CastillaL, YanofskyMF (2000b). An ancestral MADS-box gene duplication occurred before the divergence of plants and animals.Proc Natl Acad Sci USA 97, 5328-5333. DOI:10.1073/pnas.97.10.5328URL [本文引用: 1]
[4]
AroraR, AgarwalP, RayS, SinghAK, SinghVP, TyagiAK, KapoorS (2007). MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress.BMC Genomics 8, 242. DOI:10.1186/1471-2164-8-242PMID:17640358URLpAbstract/p pBackground/p pMADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, itArabidopsis/it. Though there have been some studies in rice as well, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of rice genome sequencing. Furthermore, owing to the role of MADS-box family in flower development, an analysis involving structure, expression and functional aspects of MADS-box genes in rice and itArabidopsis /itwas required to understand the role of this gene family in reproductive development./p pResults/p pA genome-wide molecular characterization and microarray-based expression profiling of the genes encoding MADS-box transcription factor family in rice is presented. Using a thorough annotation exercise, 75 MADS-box genes have been identified in rice and categorized into MIKCsupc/sup, MIKC*, M , M and M groups based on phylogeny. Chromosomal localization of these genes reveals that 16 MADS-box genes, mostly MIKCsupc/sup-type, are located within the duplicated segments of the rice genome, whereas most of the M-type genes, 20 in all, seem to have resulted from tandem duplications. Nine members belonging to the M group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven genes under stress conditions is also evident. An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and itArabidopsis/it./p pConclusion/p pOnly a limited number of MADS genes have been functionally validated in rice. A comprehensive annotation and transcriptome profiling undertaken in this investigation adds to our understanding of the involvement of MADS-box family genes during reproductive development and stress in rice and also provides the basis for selection of candidate genes for functional validation studies./p [本文引用: 5]
ChangYY, ChiuYF, WuJW, YangCH (2009). Four orchid (Oncidium Gower Ramsey) AP1/AGL9-like MADS box genes show novel expression patterns and cause different effects on floral transition and formation in Arabidopsis thaliana. Plant Cell Physiol 50, 1425-1438. [本文引用: 2]
[8]
ChengF, LiuSY, WuJ, FangL, SunSL, LiuB, LiPX, HuaW, WangXW (2011). BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 11, 136. DOI:10.1186/1471-2229-11-136PMID:21995777URLpAbstract/p pBackground/p pBrassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous aspects of plant biology, specifically for the analysis of genome evolution following polyploidy, so it is also very important for scientific research. Now, the genome of itBrassica rapa /ithas already been assembled, it is the time to do deep mining of the genome data./p pDescription/p pBRAD, the Brassica database, is a web-based resource focusing on genome scale genetic and genomic data for important Brassica crops. BRAD was built based on the first whole genome sequence and on further data analysis of the Brassica A genome species, itBrassica rapa /it(Chiifu-401-42). It provides datasets, such as the complete genome sequence of itB. rapa/it, which was itde novo /itassembled from Illumina GA II short reads and from BAC clone sequences, predicted genes and associated annotations, non coding RNAs, transposable elements (TE), itB. rapa /itgenes orthologous to those in itA. thaliana/it, as well as genetic markers and linkage maps. BRAD offers useful searching and data mining tools, including search across annotation datasets, search for syntenic or non-syntenic orthologs, and to search the flanking regions of a certain target, as well as the tools of BLAST and Gbrowse. BRAD allows users to enter almost any kind of information, such as a itB. rapa /itor itA. thaliana /itgene ID, physical position or genetic marker./p pConclusion/p pBRAD, a new database which focuses on the genetics and genomics of the Brassica plants has been developed, it aims at helping scientists and breeders to fully and efficiently use the information of genome data of Brassica plants. BRAD will be continuously updated and can be accessed through urlhttp://brassicadb.org/url./p [本文引用: 1]
[9]
DayRC, HerridgeRP, AmbroseBA, MacknightRC (2008). Transcriptome analysis of proliferating Arabidopsis endos- perm reveals biological implications for the control of syn- cytial division, cytokinin signaling, and gene expression regulation.Plant Physiol 148, 1964-1984. DOI:10.4161/psb.4.9.9461PMID:18923020URLDuring the early stages of Arabidopsis seed development, the endosperm is syncytial and proliferates rapidly through multiple rounds of mitosis in the absence of cytokinesis and cell wall formation. This stage of endosperm development is important in determining seed viability and size. To identify genes involved in syncytial endosperm development, we analyzed the endosperm transcriptome, obtained using laser capture microdissection of developing seeds at 4 days after pollination. Our results support the idea that similar sets of genes are required for conventional somatic mitosis with cytokinesis and syncytial proliferation. Furthermore, we identify cytoskeleton associated genes that may act to facilitate syncytial development thereby providing an important resource for further characterization of the processes involved in syncytial endosperm development. [本文引用: 1]
[10]
De BodtS, RaesJ, Van de PeerY, Thei?enG (2003). And then there were many: MADS goes genomic.Trends Plant Sci 8, 475-483. DOI:10.1016/j.tplants.2003.09.006PMID:14557044URLDuring the past decade, MADS-box genes have become known as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by bioinformatics, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Therefore, the recent advances in comparative and functional genomics should enable researchers to identify the full range of MADS-box gene functions, which should help us significantly in developing a better understanding of plant development and evolution. [本文引用: 1]
[11]
Díaz-RiquelmeJ, LijavetzkyD, Martínez-ZapaterJM, CarmonaMJ (2009). Genome-wide analysis of MIKCC- type MADS box genes in grapevine.Plant Physiol 149, 354-369. DOI:10.1104/pp.108.131052URL [本文引用: 2]
[12]
DoebleyJ, LukensL (1998). Transcriptional regulators and the evolution of plant form.Plant Cell 10, 1075-1082. DOI:10.2307/3870712PMID:9668128URLCirculation. 2000 Jul 25;102(4):368-70. Editorial [本文引用: 1]
[13]
DuanWK, SongXM, LiuTK, HuangZN, RenJ, HouXL, LiY (2015). Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage). Mol Genet Genomics 290, 239-255. DOI:10.1007/s00438-014-0912-7PMID:25216934URLThe MADS-box gene family is an ancient and well-studied transcription factor family that functions in almost every developmental process in plants. There are a number of reports about the MADS-box family in different plant species, but systematic analysis of the MADS-box transcription factor family in Brassica rapa (Chinese cabbage) is still lacking. In this study, 160 MADS-box transcription factors were identified from the entire Chinese cabbage genome and compared with the MADS-box factors from 21 other representative plant species. A detailed list of MADS proteins from these 22 species was sorted. Phylogenetic analysis of the BrMADS genes, together with their Arabidopsis and rice counterparts, showed that the BrMADS genes were categorised into type I (M , M , M ) and type II (MIKC C , MIKC*) groups, and the MIKC C proteins were further divided into 13 subfamilies. The Chinese cabbage type II group has 95 members, which is twice as much as the Arabidopsis type II group, indicating that the Chinese cabbage type II genes have been retained more frequently than the type I genes. Finally, RNA-seq transcriptome data and quantitative real-time PCR analysis revealed that BrMADS genes are expressed in a tissue-specific manner similar to Arabidopsis . Interestingly, a number of BrMIKC genes showed responses to different abiotic stress treatments, suggesting a function for some of the genes in these processes as well. Taken together, the characterization of the B. rapa MADS-box family presented here, will certainly help in the selection of appropriate candidate genes and further facilitate functional studies in Chinese cabbage. [本文引用: 3]
[14]
EdgerPP, PiresJC (2009). Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes.Chromosome Res 17, 699-717. DOI:10.1007/s10577-009-9055-9URL [本文引用: 1]
[15]
FanCM, WangX, WangYW, HuRB, ZhangXM, ChenJX, FuYF (2013). Genome-wide expression analysis of soy- bean MADS genes showing potential function in the seed development.PLoS One 8, e62288. DOI:10.1371/journal.pone.0062288PMID:23638026URLThe MADS family is an ancient and best-studied transcription factor and plays fundamental roles in almost every developmental process in plants. In the plant evolutionary history, the whole genome duplication (WGD) events are important not only to the plant species evolution, but to expansion of members of the gene families. Soybean as a model legume crop has experience three rounds of WGD events. Members of some MIKCCsubfamilies, such as SOC, AGL6, SQUA, SVP, AGL17 and DEF/GLO, were expanded after soybean three rounds of WGD events. And some MIKCCsubfamilies, MIKC* and type I MADS families had experienced faster birth-and-death evolution and their traces before theGlycineWGD event were not found. Transposed duplication played important roles in tandem arrangements among the members of different subfamilies. According to the expression profiles of type I and MIKC paralog pair genes, the fates of MIKC paralog gene pairs were subfunctionalization, and the fates of type I MADS paralog gene pairs were nonfunctionalization. 137 out of 163MADSgenes were close to 186 loci within 2 Mb genomic regions associated with seed-relative QTLs, among which 115 genes expressed during the seed development. Although MIKCCgenes kept the important and conserved functions of the flower development, most MIKCCgenes showed potentially essential roles in the seed development as well as the type I MADS. [本文引用: 1]
[16]
FangSC, FernandezDE (2002). Effect of regulated over- expression of the MADS domain factor AGL15 on flower senescence and fruit maturation.Plant Physiol 130, 78-89. DOI:10.1104/pp.004721PMID:12226488URLWe have examined the effect of regulated overexpression of AGL15, a member of the MADS domain family of regulatory factors, on reproductive tissues. Using molecular and physiological markers, we show that constitutive overexpression of AGL15 in Arabidopsis leads to delay and down-regulation of senescence programs in perianth organs and developing fruits and alters the process of seed desiccation. Through genetic crosses, we show that the rate of water loss in the maturing seeds is dictated by the genetic composition and physiological state of the maternal tissue, rather than the embryo. To define the developmental time and/or place when senescence programs are most affected by elevated AGL15 levels, we expressed AGL15 under the control of various promoters. Expression during senescence or in abscission zone cells did not produce delays in floral organ senescence or abscission. Using a glucocorticoid-inducible expression system, we show that an increase in AGL15 levels around the time of flower opening is necessary to delay senescence and increase floral organ longevity. [本文引用: 3]
[17]
FinnRD, BatemanA, ClementsJ, CoggillP, EberhardtRY, EddySR, HegerA, HetheringtonK, HolmL, MistryJ, SonnhammerELL, TateJ, PuntaM (2014). Pfam: the protein families database.Nucleic Acids Res 42, D222-D230. DOI:10.1093/nar/gkt1223PMID:3965110URLPfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. [本文引用: 1]
[18]
GanYB, FilleurS, RahmanA, GotensparreS, FordeBG (2005). Nutritional regulation of ANR1 and other root- expressed MADS-box genes in Arabidopsis thaliana. Planta 222, 730-742. [本文引用: 1]
[19]
GramzowL, RitzMS, Thei?enG (2010). On the origin of MADS-domain transcription factors.Trends Genet 26, 149-153. DOI:10.1016/j.tig.2010.01.004PMID:20219261URLMADS-domain transcription factors are involved in signal transduction and developmental control in plants, animals and fungi. Because their diversification is linked to the origin of novelties in multicellular eukaryotes, the early evolution of MADS-domain proteins is of interest, but has remained enigmatic. Employing whole genome sequence information and remote homology detection methods, we demonstrate that the MADS domain originated from a region of topoisomerases IIA subunit A. Furthermore, we provide evidence that gene duplication occurred in the lineage that led to the MRCA of extant eukaryotes, giving rise to SRF-like and MEF2-like MADS-box genes. [本文引用: 1]
[20]
GreenupA, PeacockWJ, DennisES, TrevaskisB (2009). The molecular biology of seasonal flowering-responses in Arabidopsis and the cereals.Ann Bot 103, 1165-1172. DOI:10.1093/aob/mcp063PMID:2685306URLBackground In arabidopsis (Arabidopsis thaliana), FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) play key roles in regulating seasonal flowering-responses to synchronize flowering with optimal conditions. FT is a promoter of flowering activated by long days and by warm conditions. FLC represses FT to delay flowering until plants experience winter. Scope The identification of genes controlling flowering in cereals allows comparison of the molecular pathways controlling seasonal flowering-responses in cereals with those of arabidopsis. The role of FT has been conserved between arabidopsis and cereals; FT-like genes trigger flowering in response to short days in rice or long days in temperate cereals, such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Many varieties of wheat and barley require vernalization to flower but FLC-like genes have not been identified in cereals. Instead, VERNALIZATION2 (VRN2) inhibits long-day induction of FT-like 1 (FT1) prior to winter. VERNALIZATION 1 (VRN1) is activated by low-temperatures during winter to repress VRN2 and to allow the long-day response to occur in spring. In rice (Oryza sativa) a VRN2-like gene Ghd7, which influences grain number, plant height and heading date, represses the FT-like gene Heading date 3a (Hd3a) in long days, suggesting a broader role for VRN2-like genes in regulating day-length responses in cereals. Other genes, including Early heading date (Ehd1), Oryza sativa MADS51 (OsMADS51) and INDETERMINATE 1 (OsID1) up-regulate Hd3a in short days. These genes might account for the different day-length response of rice compared with the temperate cereals. No genes homologous to VRN2, Ehd1, Ehd2 or OsMADS51 occur in arabidopsis. Conclusions It seems that different genes regulate FT orthologues to elicit seasonal flowering-responses in arabidopsis and the cereals. This highlights the need for more detailed study into the molecular basis of seasonal flowering-responses in cereal crops or in closely related model plants such as Brachypodium distachyon. [本文引用: 2]
[21]
GrimpletJ, Martínez-ZapaterJM, CarmonaMJ (2016). Structural and functional annotation of the MADS-box transcription factor family ingrapevine.BMC Genomics 17, 80. DOI:10.1186/s12864-016-2398-7PMID:4729134URLMADS-box genes encode transcription factors that are involved in developmental control and signal transduction in eukaryotes. In plants, they are associated to numerous development processes most notably those related to reproductive development: flowering induction, specification of inflorescence and flower meristems, establishment of flower organ identity, as well as regulation of fruit, seed and embryo development. Genomic analyses of MADS-box genes in different plant species are providing new relevant information on the function and evolution of this transcriptional factor family. We have performed a true genome-wide analysis of the complete set of MADS-box genes in grapevine (Vitis vinifera), analyzed their expression pattern and establish their phylogenetic relationships (including MIKC* and type I MADS-box) with genes from 16 other plant species. This study was integrated to previous works on the family in grapevine. A total of 90 MADS-box genes were detected in the grapevine reference genome by completing current gene annotations with a genome-wide analysis based on sequence similarity. We performed a thorough in-depth curation of all gene models and combined the results with gene expression information including RNAseq data to clarifying the expression of newly identified genes and improve their functional characterization. Curated data were uploaded to the ORCAE database for grapevine in the frame of the grapevine genome curation effort. This approach resulted in the identification of 30 additional MADS box genes. Among them, ten new MIKCCgenes were identified, including a potential new group of short proteins similar to the SVP protein subfamily. The MIKC* subgroup contains six genes in grapevine that can be grouped in the S (4 genes) and P (2 genes) clades, showing less redundancy than that observed inArabidopsis thaliana. Expression pattern of these genes in grapevine is compatible with a role in male gametophyte development. Most of the identified new genes belong to the type I MADS-box genes and were classified as members of the M and M subclasses. Ours analyses indicate that only few members of type I genes in grapevine have homology in other species and that species-specific clades appeared both in the M and M subclasses. On the other hand, as deduced from the phylogenetic analysis with other plant species, genes that can be crucial for development of central cell, endosperm and embryos seems to be conserved in plants. The genome analysis of MADS-box genes in grapevine, the characterization of their pattern of expression and the phylogenetic analysis with other plant species allowed the identification of new MADS-box genes not yet described in other plant species as well as basic characterization of their possible role, particularly in the case of type I and MIKC* genes. The online version of this article (doi:10.1186/s12864-016-2398-7) contains supplementary material, which is available to authorized users. [本文引用: 1]
[22]
HemmingMN, TrevaskisB (2011). Make hay when the sun shines: the role of MADS-box genes intemperature- dependant seasonal flowering responses.Plant Sci 180, 447-453. DOI:10.1016/j.plantsci.2010.12.001PMID:21421391URLMADS-box transcription factors specify plant meristem identity. In doing so, they determine when floral organs are produced at the shoot apex and control the timing of flowering. The transcriptional activity of key MADS-box genes is controlled by temperature in many plants, and this synchronises flowering with changing seasons. Here we review how seasonal temperature variation influences the developmental programme of plants via transcriptional regulation of MADS-box genes. In particular we examine the role of MADS-box genes in regulating the acceleration of flowering by vernalization (prolonged periods of cold), using FLOWERING LOCUS C of Arabidopsis and VERNALIZATION1 of cereals as examples. A potential role for SHORT VEGETATIVE PHASE-like genes in controlling winter bud dormancy is also examined, as are potential roles for MADS-box genes in regulating developmental responses to elevated growth temperatures. We conclude that understanding how temperature regulates the transcription of MADS-box genes provides insight into how seasonal fluctuations in temperature influence plant development. Plant breeders may be able to use natural variation in temperature-responsive MADS-box genes to breed future crop varieties. [本文引用: 1]
[23]
ImminkRGH, KaufmannK, AngenentGC (2010). The ‘ABC’ of MADS domain protein behaviour and interactions.Semin Cell Dev Biol 21, 87-93. DOI:10.1016/j.semcdb.2009.10.004PMID:19883778URLDevelopment of eudicot flowers is under tight developmental control by genes belonging to the MADS box transcription factor family, as is nicely represented by the well-known ABC model of floral organ development. During the last two decades enormous progress has been made in our understanding of the molecular mechanisms underlying the combinatorial activity of the encoded MADS domain proteins. Here, we review how various state-of-the-art technologies were implemented in order to unravel the protein rotein interaction network for the plant MADS domain transcription factor family. In addition, results from in planta studies of MADS domain protein behaviour and interactions will be discussed. Dimerisation and higher-order complex formation of MADS domain proteins appear to be instrumental and essential for floral organ identity determination and the precise regulation of specific target gene sets. According to the current molecular model, the floral MADS proteins assemble into quaternary complexes consisting of two dimers, which is mediated by the E class proteins. Furthermore, evidence has been provided that MADS protein rotein interactions specify DNA binding capacity, inter- and intracellular localisations of the proteins and the biological function of the constituted transcription complexes. [本文引用: 1]
[24]
JinJP, ZhangH, KongL, GaoG, LuoJC (2014). Plant TFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors.Nucleic Acids Res 42, D1182-D1187. DOI:10.1093/nar/gkt1016PMID:24174544URLWith the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences. [本文引用: 1]
[25]
KawaharaY, de la BastideM, HamiltonJP, KanamoriH, McCombieWR, OuyangS, SchwartzDC, TanakaT, WuJZ, ZhouSG, ChildsKL, DavidsonRM, LinHN, Quesada-OcampoL, VaillancourtB, SakaiH, LeeSS, KimJ, NumaH, ItohT, BuellCR, MatsumotoT (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6, 4. DOI:10.1186/1939-8433-6-4PMID:24280374URLAbstractBackgroundRice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice japonicaResultsThe Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice ConclusionsA revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. [本文引用: 1]
[26]
KofujiR, SumikawaN, YamasakiM, KondoK, UedaK, ItoM, HasebeM (2003). Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses.Mol Biol Evol 20, 1963-1977. DOI:10.1093/molbev/msg216PMID:12949148URLMADS-box genes encode transcription factors involved in various important aspects of development and differentiation in land plants, metazoans, and other organisms. Three types of land plant MADS-box genes have been reported. MIKCC- and MIKC*-type genes both contain conserved MADS and K domains but have different exon/intron structures. M-type genes lack a K domain. Most MADS-box genes previously analyzed in land plants are expressed in the sporophyte (diploid plant body); few are expressed in the gametophyte (haploid plant body). Land plants are believed to have evolved from a gametophyte (haploid)-dominant ancestor without a multicellular sporophyte (diploid plant body); most genes expressed in the sporophyte probably originated from those used in the gametophyte during the evolution of land plants. To analyze the evolution and diversification of MADS-box genes in land plants, gametophytic MADS-box genes were screened using macroarray analyses for 105 MADS-box genes found in the Arabidopsis genome. Eight MADS-box genes were predominantly expressed in pollen, the male gametophyte; all but one of their expression patterns was confirmed by Northern analyses. Analyses of the exon/intron structure of these seven genes revealed that they included two MIKCC-type, one M-type, and four MIKC*-type MADS-box genes. Previously, MIKC*-type genes have been reported only from a moss and a club moss, and this is the first record in seed plants. These genes can be used to investigate the unknown ancestral functions of MADS-box genes in land plants. The macroarray analyses did not detect expression of 56 of 61 M-type MADS-box genes in any tissues examined. A phylogenetic tree including all three types of Arabidopsis MADS-box genes with representative genes from other organisms showed that M-type genes were polyphyletic and that their branch lengths were much longer than for the other genes. This finding suggests that most M-type genes are pseudogenes, although further experiments are necessary to confirm this possibility. Our global phylogenetic analyses of MADS-box genes did not support the previous classification of MADS-box genes into type I and II groups, based on smaller scale analyses. An evolutionary scenario for the evolution of MADS-box genes in land plants is discussed. [本文引用: 1]
[27]
KrzywinskiM, ScheinJ, BirolI, ConnorsJ, GascoyneR, HorsmanD, JonesSJ, MarraMA (2009). Circos: an information aesthetic for comparative genomics.Genome Res 19, 1639-1645. DOI:10.1101/gr.092759.109URL [本文引用: 1]
[28]
LetunicI, DoerksT, BorkP (2015). SMART: recent upda- tes, new developments and status in 2015.Nucleic Acids Res 43, D257-D260. DOI:10.1093/nar/gku949PMID:25300481URLAbstract SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de/) providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. In the current version, SMART contains manually curated models for more than 1200 protein domains, with 090804 200 new models since our last update article. The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million. SMART's 'Genomic' mode, which annotates proteins from completely sequenced genomes was greatly expanded and now includes 2031 species, compared to 1133 in the previous release. SMART analysis results pages have been completely redesigned and include links to several new information sources. A new, vector-based display engine has been developed for protein schematics in SMART, which can also be exported as high-resolution bitmap images for easy inclusion into other documents. Taxonomic tree displays in SMART have been significantly improved, and can be easily navigated using the integrated search engine. 0008 The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. [本文引用: 1]
MaereS, De BodtS, RaesJ, CasneufT, Van MontaguM, KuiperM, Van de PeerY (2005). Modeling gene and genome duplications in eukaryotes.Proc Natl Acad Sci USA 102, 5454-5459. DOI:10.1073/pnas.0501102102URL [本文引用: 1]
[32]
MasieroS, ColomboL, GriniPE, SchnittgerA, KaterMM (2011). The emerging importance of type I MADS box transcription factors for plant reproduction.Plant Cell 23, 865-872. DOI:10.1105/tpc.110.081737PMID:21378131URLBased on their evolutionary origin, MADS box transcription factor genes have been divided into two classes, namely, type I and II. The plant-specific type II MIKC MADS box genes have been most intensively studied and shown to be key regulators of developmental processes, such as meristem identity, flowering time, and fruit and seed development. By contrast, very little is known about type I MADS domain transcription factors, and they have not attracted interest for a long time. A number of recent studies have now indicated a key regulatory role for type I MADS box factors in plant reproduction, in particular in specifying female gametophyte, embryo, and endosperm development. These analyses have also suggested that type I MADS box factors are decisive for setting reproductive boundaries between species. [本文引用: 1]
[33]
MitchellA, ChangHY, DaughertyL, FraserM, HunterS, LopezR, McAnullaC, McMenaminC, NukaG, PesseatS, Sangrador-VegasA, ScheremetjewM, RatoC, YongSY, BatemanA, PuntaM, AttwoodTK, SigristCJA, RedaschiN, RivoireC, XenariosI, KahnD, GuyotD, BorkP, LetunicI, GoughJ, OatesM, HaftD, HuangHZ, NataleDA, WuCH, OrengoC, SillitoeI, MiHY, ThomasPD, FinnRD (2015). The InterPro protein families data- base: the classification resource after 15 years.Nucleic Acids Res 43, D213-D221. DOI:10.1093/nar/gku1243PMID:4383996URLThe InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36,766 member database signatures integrated into 26,238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012. [本文引用: 1]
[34]
NagaharuU (1935). Genome analysis in Brassica with spe- cial reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot 7, 389-452. [本文引用: 1]
[35]
NakanoT, SuzukiK, FujimuraT, ShinshiH (2006). Genome- wide analysis of the ERF gene family in Arabidopsis and rice.Plant Physiol 140, 411-432. DOI:10.1104/pp.105.073783URL [本文引用: 1]
[36]
NamJ, dePamphilisCW, MaH, NeiM (2003). Antiquity and evolution of the MADS-box gene family controlling flower development in plants.Mol Biol Evol 20, 1435-1447. DOI:10.1093/molbev/msg152PMID:12777513URLAbstract MADS-box genes in plants control various aspects of development and reproductive processes including flower formation. To obtain some insight into the roles of these genes in morphological evolution, we investigated the origin and diversification of floral MADS-box genes by conducting molecular evolutionary genetics analyses. Our results suggest that the most recent common ancestor of today's floral MADS-box genes evolved roughly 650 MYA, much earlier than the Cambrian explosion. They also suggest that the functional classes T (SVP), B (and Bs), C, F (AGL20 or TM3), A, and G (AGL6) of floral MADS-box genes diverged sequentially in this order from the class E gene lineage. The divergence between the class G and E genes apparently occurred around the time of the angiosperm/gymnosperm split. Furthermore, the ancestors of three classes of genes (class T genes, class B/Bs genes, and the common ancestor of the other classes of genes) might have existed at the time of the Cambrian explosion. We also conducted a phylogenetic analysis of MADS-domain sequences from various species of plants and animals and presented a hypothetical scenario of the evolution of MADS-box genes in plants and animals, taking into account paleontological information. Our study supports the idea that there are two main evolutionary lineages (type I and type II) of MADS-box genes in plants and animals. [本文引用: 1]
[37]
ParenicováL, de FolterS, KiefferM, HornerDS, FavalliC, BusscherJ, CookHE, IngramRM, KaterMM, DaviesB, AngenentGC, ColomboL (2003). Molecular and phylo- genetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world.Plant Cell 15, 1538-1551. DOI:10.1105/tpc.011544URL [本文引用: 5]
[38]
PuruggananMD, RounsleySD, SchmidtRJ, YanofskyMF (1995). Molecular evolution of flower development: diver- sification of the plant MADS-box regulatory gene family.Genetics 140, 345-356. [本文引用: 1]
[39]
SahaG, ParkJI, JungHJ, AhmedNU, KayumMA, ChungMY, HurY, ChoYG, WatanabeM, NouIS (2015). Genome-wide identification and characterization of MADS- box family genes related to organ development and stress resistance in Brassica rapa. BMC Genomics 16, 178. DOI:10.1186/s12864-015-1349-zPMID:4422603URLAbstract Background MADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development. Studies on stress resistance-related functions of MADS-box genes are very limited and no such functional studies in Brassica rapa have been reported. To gain insight into this gene family and to elucidate their roles in organ development and stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in B. rapa. Results Whole-genome survey of B. rapa revealed 167 MADS-box genes, which were categorized into type I (M , M and M ) and type II (MIKCc and MIKC*) based on phylogeny, protein motif structure and exon-intron organization. Expression analysis of 89 MIKCc and 11 MIKC* genes was then carried out. In addition to those with floral and vegetative tissue expression, we identified MADS-box genes with constitutive expression patterns at different stages of flower development. More importantly, from a low temperature-treated whole-genome microarray data set, 19 BrMADS genes were found to show variable transcript abundance in two contrasting inbred lines of B. rapa. Among these, 13 BrMADS genes were further validated and their differential expression was monitored in response to cold stress in the same two lines via qPCR expression analysis. Additionally, the set of 19 BrMADS genes was analyzed under drought and salt stress, and 8 and 6 genes were found to be induced by drought and salt, respectively. Conclusion The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MADS-box genes in stress resistance in addition to their growth and developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate genes for genetic engineering of B. rapa. [本文引用: 3]
[40]
ShaoSQ, LiBY, ZhangZT, ZhouY, JiangJ, LiXB (2010). Expression of a cotton MADS-box gene is regulated in anther development and in response to phytohormone sig- naling.J Genet Genomics 37, 805-816. DOI:10.1016/S1673-8527(09)60098-9PMID:21193159URLMADS-box gene family encodes a large number and variety of transcription regulators in plants. In this study, a cDNA, GhMADS9, encoding a typical MADS protein with 230 amino acids was isolated from cotton flower cDNA library. Subsequently, a 1,623 bp genomic DNA fragment of GhMADS9 gene was isolated in cotton by PCR. Compared with its cDNA sequence, six introns were found in GhMADS9 gene. Fluorescent microscopy indicated that GhMADS9 protein localized in the nucleus. Transactivation activity assay in yeast cells revealed that GhMADS9 protein did not show transcriptional activation. Quantitative RT-PCR analysis showed that GhMADS9 was specially expressed in cotton anthers. Further in situ hybridization analysis demonstrated that strong expression of GhMADS9 gene was detected in developing pollens, but no or weak signals were found in the other anther tissues. Furthermore, GhMADS9 expression was dramatically up-regulated in anthers with abscisic acid (ABA) treatment, whereas its activity was down-regulated when treated by gibberellin (GA3). Collectively, our results suggest that GhMADS9 is a transcription factor and might be involved in cotton anther/pollen development and in response to ABA and GA3 signaling. [本文引用: 1]
[41]
ShoreP, SharrocksAD (1995). The MADS-box family of transcription factors.Eur J Biochem 229, 1-13. DOI:10.1111/j.1432-1033.1995.0001l.xPMID:7744019URLAbstract The MADS-box family of transcription factors has been defined on the basis of primary sequence similarity amongst numerous proteins from a diverse range of eukaryotic organisms including yeasts, plants, insects, amphibians and mammals. The MADS-box is a conserved motif found within the DNA-binding domains of these proteins and the name refers to four of the originally identified members: MCM1, AG, DEFA and SRF. Several proteins within this family have significant biological roles. For example, the human serum-response factor (SRF) is involved in co-ordinating transcription of the protooncogene c-fos, whilst MCM1 is central to the transcriptional control of cell-type specific genes and the pheromone response in the yeast Saccharomyces cerevisiae. The RSRF/MEF2 proteins comprise a sub-family of this class of transcription factors which are key components in muscle-specific gene regulation. Moreover, in plants, MADS-box proteins such as AG, DEFA and GLO play fundamental roles during flower development. The MADS-box is a contiguous conserved sequence of 56 amino acids, of which 9 are identical in all family members described so far. Several members have been shown to form dimers and consequently two functional regions within the MADS-box have been defined. The N-terminal half is the major determinant of DNA-binding specificity whilst the C-terminal half is necessary for dimerisation. This organisation allows the potential formation of numerous proteins, with subtly different DNA-binding specificities, from a limited number of genes by heterodimerisation between different MADS-box proteins. The majority of MADS-box proteins bind similar sites based on the consensus sequence CC(A/T)6GG although each protein apparently possesses a distinct binding specificity. Moreover, several MADS-box proteins specifically recruit other transcription factors into multi-component regulatory complexes. Such interactions with other proteins appears to be a common theme within this family and play a pivotal role in the regulation of target genes. [本文引用: 1]
[42]
ShuYJ, YuDS, WangD, GuoDL, GuoCH (2013). Genome- wide survey and expression analysis of the MADS-box gene family in soybean.Mol Biol Rep 40, 3901-3911. DOI:10.1007/s11033-012-2438-6PMID:23559340URLMADS-box genes encode important transcription factors in plants that are involved in many processes during plant growth and development. An investigation of the soybean genome revealed 106 putative MADS-box genes. These genes were classified into two classes, type I and type II, based on phylogenetic analysis. The soybean type II group has 72 members, which is higher than that of Arabidopsis, indicating that soybean type II genes have undergone a higher rate of duplication and/or a lower rate of gene loss after duplication. Soybean MADS-box genes are present on all chromosomes. Like Arabidopsis and rice MADS-box genes, soybean MADS-box genes expanded through tandem gene duplication and segmental duplication events. There are many duplicate genes distributed across the soybean genome, with two genomic regions, i.e., MADS-box gene hotspots, where MADS-box genes with high degrees of similarity are clustered. Analysis of high-throughput sequencing data from soybean at different developmental stages and in different tissues revealed that MADS-box genes are expressed in embryos of various stages and in floral buds. This expression pattern suggests that soybean MADS-box genes play an important role in soybean growth and floral development. [本文引用: 2]
TangHB, BowersJE, WangXY, MingR, AlamM, Pater- sonAH (2008). Synteny and collinearity in plant genomes.Science 320, 486-488. DOI:10.1126/science.1153917PMID:18436778URLCorrelated gene arrangements among taxa provide a valuable framework for inference of shared ancestry of genes and for the utilization of findings from model organisms to study less-well-understood systems. In angiosperms, comparisons of gene arrangements are complicated by recurring polyploidy and extensive genome rearrangement. New genome sequences and improved analytical approaches are clarifying angiosperm evolution and revealing patterns of differential gene loss after genome duplication and differential gene retention associated with evolution of some morphological complexity. Because of variability in DNA substitution rates among taxa and genes, deviation from collinearity might be a more reliable phylogenetic character. [本文引用: 1]
TheissenG, BeckerA, Di RosaA, KannoA, KimJT, MünsterT, WinterKU, SaedlerH (2000). A short history of MADS-box genes in plants.Plant Mol Biol 42, 115-149. DOI:10.1023/A:1006332105728PMID:10688133URLAbstract Evolutionary developmental genetics (evodevotics) is a novel scientific endeavor which assumes that changes in developmental control genes are a major aspect of evolutionary changes in morphology. Understanding the phylogeny of developmental control genes may thus help us to understand the evolution of plant and animal form. The principles of evodevotics are exemplified by outlining the role of MADS-box genes in the evolution of plant reproductive structures. In extant eudicotyledonous flowering plants, MADS-box genes act as homeotic selector genes determining floral organ identity and as floral meristem identity genes. By reviewing current knowledge about MADS-box genes in ferns, gymnosperms and different types of angiosperms, we demonstrate that the phylogeny of MADS-box genes was strongly correlated with the origin and evolution of plant reproductive structures such as ovules and flowers. It seems likely, therefore, that changes in MADS-box gene structure, expression and function have been a major cause for innovations in reproductive development during land plant evolution, such as seed, flower and fruit formation. [本文引用: 1]
WeiB, ZhangRZ, GuoJJ, LiuDM, LiAL, FanRC, MaoL, ZhangXQ (2014). Genome-wide analysis of the MADS- box gene family in Brachypodium distachyon. PLoS One 9, e84781. [本文引用: 2]
[50]
WeiX, WangLH, YuJY, ZhangYX, LiDH, ZhangXR (2015). Genome-wide identification and analysis of the MADS-box gene family insesame.Gene 569, 66-76. DOI:10.1016/j.gene.2015.05.018PMID:25967387URL61Mβ and AGL6-clade of MIKCC-type MADS-box genes were absent in sesame genome.61Type II MADS-box genes in sesame had more complex structures than type I genes.61MIKCC-type MADS-box genes in sesame play significant roles in flower and seed development. [本文引用: 1]
[51]
WoodhouseMR, ChengF, PiresJC, LischD, FreelingM, WangXW (2014). Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids.Proc Natl Acad Sci USA 111, 5283-5288. DOI:10.1073/pnas.1402475111PMID:24706847URLWhole-genome duplications happen repeatedly in a typical flowering plant lineage. Following most ancient tetraploidies, the two subgenomes are distinguishable because one subgenome, the dominant subgenome, tends to have more genes than the other subgenome. Additionally, among retained pairs, the gene on the dominant subgenome tends to be expressed more than its recessive homeolog. Using comparative genomics, we show that genome dominance is heritable. The dominant subgenome of one postpolyploidy event remains dominant through a subsequent polyploidy event. We show that transposon-derived 24-nt RNAs target and cover the upstream region of retained genes preferentially when located on the recessive subgenome, and with little regard for a gene's level of expression. We hypothesize that small RNA (smRNA)-mediated silencing of transposons near genes causes position-effect down-regulation. Unlike 24-nt smRNA coverage, transposon coverage tracks gene expression, so not all transposons behave identically. We propose that successful ancient tetraploids begin as wide crosses between two lines, each evolved for different tradeoffs between transposon silencing and negative position effects on gene expression. We hypothesize that following a chaotic wide-cross/new tetraploid period, genes acquire their new expression balances based on differences in transposon coverage in the parents. We envision patches of silenceable transposon as quantitative cis-regulators of baseline transcription rate. Attractive solutions to heterosis and the C-value paradox are mentioned. [本文引用: 1]
[52]
WuestSE, VijverbergK, SchmidtA, WeissM, Gheyse- linckJ, LohrM, WellmerF, RahnenführerJ, von MeringC, GrossniklausU (2010). Arabidopsis female gametophyte gene expression map reveals similarities bet- ween plant and animal gametes.Curr Biol 20, 506-512. DOI:10.1016/j.cub.2010.01.051PMID:20226671URLThe development of multicellular organisms is controlled by differential gene expression whereby cells adopt distinct fates. A spatially resolved view of gene expression allows the elucidation of transcriptional networks that are linked to cellular identity and function. The haploid female gametophyte of flowering plants is a highly reduced organism: at maturity, it often consists of as few as three cell types derived from a common precursor []. However, because of its inaccessibility and small size, we know little about the molecular basis of cell specification and differentiation in the female gametophyte. Here we report expression profiles of all cell types in the mature 3]. A comparison of human and Highlights? Transcriptomes of the cell types in the mature Arabidopsis female gametophyte ? Egg cell enrichment of PAZ/Piwi-domain genes indicates epigenetic regulation by siRNA ? Overrepresentation of three transcription factor families in the female gametophyte ? Human and Arabidopsis egg cells are enriched in similar functional groups [本文引用: 1]
[53]
XuZD, ZhangQX, SunLD, DuDL, ChengTR, PanHT, YangWR, WangJ (2014). Genome-wide identification, characterisation and expression analysis of the MADS-box gene family in Prunus mume. Mol Genet Genomics 289, 903-920. DOI:10.1007/s00438-014-0863-zPMID:24859011URLMADS-box genes encode transcription factors that play crucial roles in plant development, especially in flower and fruit development. To gain insight into this gene family in Prunus mume , an important ornamental and fruit plant in East Asia, and to elucidate their roles in flower organ determination and fruit development, we performed a genome-wide identification, characterisation and expression analysis of MADS-box genes in this Rosaceae tree. In this study, 80 MADS-box genes were identified in P. mume and categorised into MIKC, Mα, Mβ, Mγ and Mδ groups based on gene structures and phylogenetic relationships. The MIKC group could be further classified into 12 subfamilies. The FLC subfamily was absent in P. mume and the six tandemly arranged DAM genes might experience a species-specific evolution process in P. mume . The MADS-box gene family might experience an evolution process from MIKC genes to Mδ genes to Mα, Mβ and Mγ genes. The expression analysis suggests that P. mume MADS-box genes have diverse functions in P. mume development and the functions of duplicated genes diverged after the duplication events. In addition to its involvement in the development of female gametophytes, type I genes also play roles in male gametophytes development. In conclusion, this study adds to our understanding of the roles that the MADS-box genes played in flower and fruit development and lays a foundation for selecting candidate genes for functional studies in P. mume and other species. Furthermore, this study also provides a basis to study the evolution of the MADS-box family. [本文引用: 2]
YanofskyMF, MaH, BowmanJL, DrewsGN, FeldmannKA, MeyerowitzEM (1990). The protein encoded by the Arabidopsis homeotic gene AGAMOUS resembles trans- cription factors. Nature 346, 35-39. [本文引用: 1]
[56]
YaoQY, XiaEH, LiuFH, GaoLZ (2015). Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata. Gene 557, 35-42. DOI:10.1016/j.gene.2014.12.005PMID:25481634URL61We characterized a total of 148 WRKY genes including 37 novel ones in cabbage.61Preferential retention after WGT may contribute to rapid expansion of WRKY family.61A large portion of WRKY genes exhibited patterns of tissue-specific expression.61Expression divergence of BolWRKY paralogs indicates their functional diversification. [本文引用: 1]
[57]
YuLH, MiaoZQ, QiGF, WuJ, CaiXT, MaoJL, XiangCB (2014). MADS-box transcription factor AGL21 regulates lateral root development and responds to multiple external and physiological signals.Mol Plant 7, 1653-1669. DOI:10.1093/mp/ssu088PMID:4228986URLMADS-box transcription factor AGL21 is responsive to several phytohormones as well as environmental cues and positively regulates auxin accumulation in lateral root primordia and lateral roots by enhancing local auxin biosynthesis, thus stimulating lateral root initiation and growth. Therefore, AGL21 may be involved in various environmental and physiological signals-mediated lateral root development. [本文引用: 1]
[58]
ZhangZ, LiJ, ZhaoXQ, WangJ, WongGKS, YuJ (2006). KaKs_calculator: calculating Ka and Ks through model selection and model averaging.Genomics Proteomics Bioinformatics 4, 259-263. DOI:10.1016/S1672-0229(07)60007-2PMID:5054075URLKaKs_Calculator is a software package that calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. Since existing methods for this estimation adopt their specific mutation (substitution) models that consider different evolutionary features, leading to diverse estimates, KaKs_Calculator implements a set of candidate models in a maximum likelihood framework and adopts the Akaike information criterion to measure fitness between models and data, aiming to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into this software. KaKs_Calculator, including source codes, compiled executables, and documentation, is freely available for academic use athttp://evolution.genomics.org.cn/software.htm. [本文引用: 1]
1 2012
... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ...
1 2000
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2000
... MADS-box转录因子广泛存在于酵母、植物、昆虫、线虫、低等脊椎动物和哺乳动物等真核生物体内, 其命名来自酵母(Saccharomyces cerevisiae) MCMI基因、拟南芥(Arabidopsis thaliana) AGAMOUS基因、金鱼草(Antirrhinum majus) DEFTCI基因及人类(Homo sapiens) SRF基因的首字母缩写(Purugganan et al., 1995; Shore and Sharrocks, 1995).MADS- box家族基因的典型特征是N端具有60个氨基酸的MADS-box结构域, 这一结构域是参与转录激活的重要组件.依据基因所含有结构域的类型可以将MADS-box家族基因分为两类, I型(M-type)包含α、β和γ三个亚家族, II型(MIKC-type)包含MICKC和MIKC*亚家族.MIKCC亚家族除了具有典型MADS结构域外, 还有K (Keratin-like)、I (Intervening)及C-terminal结构域(Gramzow et al., 2010).这2个亚家族在基因结构上也有区别, M-type基因序列较短, 含有较少的外显子; MIKC-type基因一般有5-8个外显子, 序列较长(Alvarez-Buylla et al., 2000b). ...
5 2007
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ... ... 随着二代测序技术的成熟, 已完成测序的物种越来越多.国内外****已经对拟南芥(Parenicová et al., 2003)、水稻(Arora et al., 2007)、大豆(Glycine max) (Shu et al., 2013)、芝麻(Sesamum indicum) (Wei et al., 2015)、二穗短柄草(Brachypodium distachyum) (Wei et al., 2014)、葡萄(Vitis vinifera) (Díaz- Riquelme et al., 2009)和梅(Armeniaca mume) (Xu et al., 2014)等物种中的MADS-box基因家族进行了探究.利用生物信息学方法, 在模式植物拟南芥中鉴定了107个MADS-box家族成员并将其分为5个亚家族: Mα (25 proteins)、Mβ (20 proteins)、Mγ (16 proteins)、Mδ (7 proteins)和MIKC (39 proteins).目前已在水稻中鉴定了72个MADS-box基因, 分为Mα (13 proteins)、Mβ (10 proteins)、Mγ (9 proteins)、MIKCC (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... ; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... 我们在PlantTFDB网站上对307个MADS-box基因进行初步预测后, 将其分为MIKC-type和M-type两个类型.参考水稻和其它物种MADS-box基因家族的分类结果(Arora et al., 2007), 我们将AGL33-like归为MIKC*.通过对分类结果进行整理, 最终将307个MADS-box基因分为两大类, 即包含125个MADS- box基因的M-type和包含182个基因的MIKC-type. ... ... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
1 2003
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
3 2014
... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ... ... ).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
2 2009
... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ...
1 2011
... 甘蓝型油菜(Brassica napus L.)基因组序列、CDS序列、蛋白质序列及其注释信息均下载自BRAD (Cheng et al., 2011)数据库(http://brassicadb.org).在Pfam (Finn et al., 2014)数据库(http://pfam.xfam.org/)中下载编号为PF00319的结构域数据. ...
1 2008
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2003
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
2 2009
... 随着二代测序技术的成熟, 已完成测序的物种越来越多.国内外****已经对拟南芥(Parenicová et al., 2003)、水稻(Arora et al., 2007)、大豆(Glycine max) (Shu et al., 2013)、芝麻(Sesamum indicum) (Wei et al., 2015)、二穗短柄草(Brachypodium distachyum) (Wei et al., 2014)、葡萄(Vitis vinifera) (Díaz- Riquelme et al., 2009)和梅(Armeniaca mume) (Xu et al., 2014)等物种中的MADS-box基因家族进行了探究.利用生物信息学方法, 在模式植物拟南芥中鉴定了107个MADS-box家族成员并将其分为5个亚家族: Mα (25 proteins)、Mβ (20 proteins)、Mγ (16 proteins)、Mδ (7 proteins)和MIKC (39 proteins).目前已在水稻中鉴定了72个MADS-box基因, 分为Mα (13 proteins)、Mβ (10 proteins)、Mγ (9 proteins)、MIKCC (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
1 1998
... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
3 2015
... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... )有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
1 2009
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 2013
... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
3 2002
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ... ... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ...
1 2014
... 甘蓝型油菜(Brassica napus L.)基因组序列、CDS序列、蛋白质序列及其注释信息均下载自BRAD (Cheng et al., 2011)数据库(http://brassicadb.org).在Pfam (Finn et al., 2014)数据库(http://pfam.xfam.org/)中下载编号为PF00319的结构域数据. ...
1 2005
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2010
... MADS-box转录因子广泛存在于酵母、植物、昆虫、线虫、低等脊椎动物和哺乳动物等真核生物体内, 其命名来自酵母(Saccharomyces cerevisiae) MCMI基因、拟南芥(Arabidopsis thaliana) AGAMOUS基因、金鱼草(Antirrhinum majus) DEFTCI基因及人类(Homo sapiens) SRF基因的首字母缩写(Purugganan et al., 1995; Shore and Sharrocks, 1995).MADS- box家族基因的典型特征是N端具有60个氨基酸的MADS-box结构域, 这一结构域是参与转录激活的重要组件.依据基因所含有结构域的类型可以将MADS-box家族基因分为两类, I型(M-type)包含α、β和γ三个亚家族, II型(MIKC-type)包含MICKC和MIKC*亚家族.MIKCC亚家族除了具有典型MADS结构域外, 还有K (Keratin-like)、I (Intervening)及C-terminal结构域(Gramzow et al., 2010).这2个亚家族在基因结构上也有区别, M-type基因序列较短, 含有较少的外显子; MIKC-type基因一般有5-8个外显子, 序列较长(Alvarez-Buylla et al., 2000b). ...
2 2009
... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ...
1 2016
... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
1 2011
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2010
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2014
... 从植物转录因子网站PlantTFDB (Jin et al., 2014) (http://planttfdb.cbi.pku.edu.cn/)下载拟南芥全部MADS-box家族成员蛋白序列.通过水稻基因组注释网站(http://rice.plantbiology.msu.edu/)下载得到水稻MADS-box蛋白序列(Kawahara et al., 2013). ...
1 2013
... 从植物转录因子网站PlantTFDB (Jin et al., 2014) (http://planttfdb.cbi.pku.edu.cn/)下载拟南芥全部MADS-box家族成员蛋白序列.通过水稻基因组注释网站(http://rice.plantbiology.msu.edu/)下载得到水稻MADS-box蛋白序列(Kawahara et al., 2013). ...
1 2003
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2009
... 通过BRAD在线检索获取拟南芥MADS-box基因在甘蓝型油菜中的共线性基因及其在染色体上的位置.用Circos (Krzywinski et al., 2009)软件将这些共线性基因的关系进行展示.用Excel 2013软件对共线性基因在染色体上的分布进行统计并作图. ...
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ... ... ).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 2013
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2005
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 2011
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ...
1 2006
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 2003
... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ...
5 2003
... 随着二代测序技术的成熟, 已完成测序的物种越来越多.国内外****已经对拟南芥(Parenicová et al., 2003)、水稻(Arora et al., 2007)、大豆(Glycine max) (Shu et al., 2013)、芝麻(Sesamum indicum) (Wei et al., 2015)、二穗短柄草(Brachypodium distachyum) (Wei et al., 2014)、葡萄(Vitis vinifera) (Díaz- Riquelme et al., 2009)和梅(Armeniaca mume) (Xu et al., 2014)等物种中的MADS-box基因家族进行了探究.利用生物信息学方法, 在模式植物拟南芥中鉴定了107个MADS-box家族成员并将其分为5个亚家族: Mα (25 proteins)、Mβ (20 proteins)、Mγ (16 proteins)、Mδ (7 proteins)和MIKC (39 proteins).目前已在水稻中鉴定了72个MADS-box基因, 分为Mα (13 proteins)、Mβ (10 proteins)、Mγ (9 proteins)、MIKCC (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ... ... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
1 1995
... MADS-box转录因子广泛存在于酵母、植物、昆虫、线虫、低等脊椎动物和哺乳动物等真核生物体内, 其命名来自酵母(Saccharomyces cerevisiae) MCMI基因、拟南芥(Arabidopsis thaliana) AGAMOUS基因、金鱼草(Antirrhinum majus) DEFTCI基因及人类(Homo sapiens) SRF基因的首字母缩写(Purugganan et al., 1995; Shore and Sharrocks, 1995).MADS- box家族基因的典型特征是N端具有60个氨基酸的MADS-box结构域, 这一结构域是参与转录激活的重要组件.依据基因所含有结构域的类型可以将MADS-box家族基因分为两类, I型(M-type)包含α、β和γ三个亚家族, II型(MIKC-type)包含MICKC和MIKC*亚家族.MIKCC亚家族除了具有典型MADS结构域外, 还有K (Keratin-like)、I (Intervening)及C-terminal结构域(Gramzow et al., 2010).这2个亚家族在基因结构上也有区别, M-type基因序列较短, 含有较少的外显子; MIKC-type基因一般有5-8个外显子, 序列较长(Alvarez-Buylla et al., 2000b). ...
3 2015
... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... ; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ... ... 甘蓝型油菜是由白菜和甘蓝(B. oleracea)天然杂交而来(Nagaharu, 1935), 是十字花科重要的油料作物.MADS-box家族基因是花期和花器官分化的主要调控因子(Fang and Fernandez, 2002; Chang et al., 2009; Greenup et al., 2009), 开花时间与花的分化是甘蓝型油菜育种和生产中重要的农艺性状, 直接决定其产量.因此, 深入研究MADS-box家族基因对于甘蓝型油菜遗传改良具有重要意义.前人利用生物信息学方法已在十字花科拟南芥中鉴定出107个MADS- box家族基因(Parenicová et al., 2003), 在白菜中鉴定出167个MADS-box家族基因(Saha et al., 2015).采用生物信息学方法, 本研究在甘蓝型油菜中鉴定出307个MADS-box基因, 是目前已报道物种中数目最多的.我们参考其它模式物种中的分类, 根据系统发育关系将这307个基因分为2类: M-type和MIKC- type.依据系统发育树(图1), M-type共包括125个基因, 可进一步分为α、β、γ三个类型; MIKC-type包含182个基因, 可分为MIKC*和MIKCC两类, MIKCC可进一步分为13个小类.白菜中AGL71-like类归于TM3- like, 我们发现甘蓝型油菜MIKC-type基因的进化树中AGL71-like并不能与TM-like归为一类.此外, 甘蓝型油菜M-type和MIKC-type MADS-box基因数目都是目前已报道物种中最多的, 且每一个小分类的基因数目也与拟南芥和水稻中的数目不同.这表明重复基因在不同物种进化过程中的保留情况不同, 因此这些不同物种中同一分类的MADS-box基因在进化过程中受到的约束不同(Nam et al., 2003; Airoldi and Davies, 2012). ...
1 2010
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 1995
... MADS-box转录因子广泛存在于酵母、植物、昆虫、线虫、低等脊椎动物和哺乳动物等真核生物体内, 其命名来自酵母(Saccharomyces cerevisiae) MCMI基因、拟南芥(Arabidopsis thaliana) AGAMOUS基因、金鱼草(Antirrhinum majus) DEFTCI基因及人类(Homo sapiens) SRF基因的首字母缩写(Purugganan et al., 1995; Shore and Sharrocks, 1995).MADS- box家族基因的典型特征是N端具有60个氨基酸的MADS-box结构域, 这一结构域是参与转录激活的重要组件.依据基因所含有结构域的类型可以将MADS-box家族基因分为两类, I型(M-type)包含α、β和γ三个亚家族, II型(MIKC-type)包含MICKC和MIKC*亚家族.MIKCC亚家族除了具有典型MADS结构域外, 还有K (Keratin-like)、I (Intervening)及C-terminal结构域(Gramzow et al., 2010).这2个亚家族在基因结构上也有区别, M-type基因序列较短, 含有较少的外显子; MIKC-type基因一般有5-8个外显子, 序列较长(Alvarez-Buylla et al., 2000b). ...
2 2013
... 随着二代测序技术的成熟, 已完成测序的物种越来越多.国内外****已经对拟南芥(Parenicová et al., 2003)、水稻(Arora et al., 2007)、大豆(Glycine max) (Shu et al., 2013)、芝麻(Sesamum indicum) (Wei et al., 2015)、二穗短柄草(Brachypodium distachyum) (Wei et al., 2014)、葡萄(Vitis vinifera) (Díaz- Riquelme et al., 2009)和梅(Armeniaca mume) (Xu et al., 2014)等物种中的MADS-box基因家族进行了探究.利用生物信息学方法, 在模式植物拟南芥中鉴定了107个MADS-box家族成员并将其分为5个亚家族: Mα (25 proteins)、Mβ (20 proteins)、Mγ (16 proteins)、Mδ (7 proteins)和MIKC (39 proteins).目前已在水稻中鉴定了72个MADS-box基因, 分为Mα (13 proteins)、Mβ (10 proteins)、Mγ (9 proteins)、MIKCC (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 2008
... 十字花科模式植物拟南芥和白菜(Brassica rapa)的MADS-box基因已被鉴定(Parenicová et al., 2003; Duan et al., 2015; Saha et al., 2015).现有的研究表明, 十字花科尤其是芸薹属植物的MADS-box基因与花器官分化(Fang and Fernandez, 2002)、开花时间(Chang et al., 2009; Greenup et al., 2009)及根尖分生组织分化(Tapia-López et al., 2008)有关.此外, 在低温和高温胁迫及赤霉素(GA)与水杨酸(SA)处理下, 这些基因的表达量也发生显著变化(Duan et al., 2015; Saha et al., 2015).甘蓝型油菜(Brassica napus)同属十字花科, 其基因组测序结果已于2014年公布(Chalhoub et al., 2014).本研究基于基因组测序结果, 对甘蓝型油菜MADS-box基因家族进行鉴定, 并利用一系列生物信息学软件对其进行注释和基本功能预测分析, 初步探究其进化关系.研究结果将为深入揭示MADS-box基因家族的生物学功能奠定重要基础. ...
1 2011
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 2000
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2010
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
2 2014
... 随着二代测序技术的成熟, 已完成测序的物种越来越多.国内外****已经对拟南芥(Parenicová et al., 2003)、水稻(Arora et al., 2007)、大豆(Glycine max) (Shu et al., 2013)、芝麻(Sesamum indicum) (Wei et al., 2015)、二穗短柄草(Brachypodium distachyum) (Wei et al., 2014)、葡萄(Vitis vinifera) (Díaz- Riquelme et al., 2009)和梅(Armeniaca mume) (Xu et al., 2014)等物种中的MADS-box基因家族进行了探究.利用生物信息学方法, 在模式植物拟南芥中鉴定了107个MADS-box家族成员并将其分为5个亚家族: Mα (25 proteins)、Mβ (20 proteins)、Mγ (16 proteins)、Mδ (7 proteins)和MIKC (39 proteins).目前已在水稻中鉴定了72个MADS-box基因, 分为Mα (13 proteins)、Mβ (10 proteins)、Mγ (9 proteins)、MIKCC (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
1 2015
... 随着二代测序技术的成熟, 已完成测序的物种越来越多.国内外****已经对拟南芥(Parenicová et al., 2003)、水稻(Arora et al., 2007)、大豆(Glycine max) (Shu et al., 2013)、芝麻(Sesamum indicum) (Wei et al., 2015)、二穗短柄草(Brachypodium distachyum) (Wei et al., 2014)、葡萄(Vitis vinifera) (Díaz- Riquelme et al., 2009)和梅(Armeniaca mume) (Xu et al., 2014)等物种中的MADS-box基因家族进行了探究.利用生物信息学方法, 在模式植物拟南芥中鉴定了107个MADS-box家族成员并将其分为5个亚家族: Mα (25 proteins)、Mβ (20 proteins)、Mγ (16 proteins)、Mδ (7 proteins)和MIKC (39 proteins).目前已在水稻中鉴定了72个MADS-box基因, 分为Mα (13 proteins)、Mβ (10 proteins)、Mγ (9 proteins)、MIKCC (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ...
1 2014
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 2010
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
2 2014
... 随着二代测序技术的成熟, 已完成测序的物种越来越多.国内外****已经对拟南芥(Parenicová et al., 2003)、水稻(Arora et al., 2007)、大豆(Glycine max) (Shu et al., 2013)、芝麻(Sesamum indicum) (Wei et al., 2015)、二穗短柄草(Brachypodium distachyum) (Wei et al., 2014)、葡萄(Vitis vinifera) (Díaz- Riquelme et al., 2009)和梅(Armeniaca mume) (Xu et al., 2014)等物种中的MADS-box基因家族进行了探究.利用生物信息学方法, 在模式植物拟南芥中鉴定了107个MADS-box家族成员并将其分为5个亚家族: Mα (25 proteins)、Mβ (20 proteins)、Mγ (16 proteins)、Mδ (7 proteins)和MIKC (39 proteins).目前已在水稻中鉴定了72个MADS-box基因, 分为Mα (13 proteins)、Mβ (10 proteins)、Mγ (9 proteins)、MIKCC (38 proteins)和MIKC* (5 proteins)五个亚家族(Parenicová et al., 2003; Arora et al., 2007).在基因组水平上用生物信息学手段鉴定MADS-box基因家族, 可为深入研究MADS-box基因的生物学功能提供重要基础. ... ... 通常来说, 起源于同一拷贝的转录因子拥有类似的基因结构(Doebley and Lukens, 1998).本研究表明, 甘蓝型油菜M-type基因通常具有较少的外显子, 序列长度也相对较短; MIKC-type基因序列普遍较长且含有较多的外显子.此外, 将307个MADS-box分为M、MIKC*和MIKCC进行保守序列预测, 结果显示, 在进化树上位于同一个小类的MADS-box蛋白所含有的motif类型几乎完全一致.以上表明这些基因在甘蓝型油菜中很可能行使类似的功能.MIKC*与MIKCC基因结构相似, 含有较多的motif和内含子, 但是缺少K-box结构域.MIKC*同时具有M-type和MIKCC的特性, 因此在早期的研究中将其归于Mδ, 后来在其它物种的MADS-box基因家族分类中将其归于MIKC- type (Parenicová et al., 2003; Arora et al., 2007; Díaz-Riquelme et al., 2009; Fan et al., 2013; Shu et al., 2013; Wei et al., 2014; Duan et al., 2015; Grimplet et al., 2016).因此, 有****认为MIKC*是从MIKCC进化到M-type的中间形态(Xu et al., 2014), 即MIKCC在长期进化选择过程中K-box结构域突变, 但保留了较多内含子, 形成了MIKC*, MIKC*在进一步的进化中丢失了内含子, 形成短序列、少内含子的M-type. ...
1 2016
... 多倍化是物种进化的重要动力, 多数高等植物在进化过程中都经历了不同水平的多倍化(Tang et al., 2008).十字花科物种都曾经历三倍化(Bowers et al., 2003).比较基因组学研究显示, 拟南芥与白菜分化自同一祖先物种.大约20-40 M, 拟南芥和白菜的共同祖先发生了1次基因组水平的复制事件, 称为α事件(Woodhouse et al., 2014).芸薹属物种在此之后又经历了1次三倍化(Chalhoub et al., 2014; Liu et al., 2014; Yang et al., 2016).在5-9 M, 甘蓝和白菜的共同祖先又经历了1次基因组水平三倍化(The Bras- sica rapa Genome Sequencing Project Consortium et al., 2011).基因组测序结果显示, 白菜与甘蓝的分化约发生在4 M (Liu et al., 2014).相对于拟南芥, 甘蓝和白菜各发生了1次基因组复制.甘蓝型油菜大约在 7 500-12 500年前由白菜和甘蓝天然杂交形成(Chalhoub et al., 2014).物种进化的实质是基因的进化, 多倍化事件是基因家族扩张的主要动力, 在多倍化之后, 基因数目呈倍数增长.依据甘蓝型油菜进化史可推断, 甘蓝型油菜MADS-box家族基因数目应多于307个.在基因组复制事件发生后, 植物为了代谢的平衡, 往往会出现大面积的基因丢失和染色体重排, 基因功能有3种分化方向: 保持原有功能、丢失原有功能及产生新功能(Nakano et al., 2006).本研究显示, 部分MADS-box基因在进化过程中丧失MADS- box结构域, 只剩下K-box结构域.还有一部分序列, 在Interpro中未注释, 也没有匹配的domain, 初步推测为假基因.因此这可能是在经历2次基因组水平的三倍化之后甘蓝型油菜中MADS-box基因家族数仅为307的原因.此外, M-type和MIKC-type在进化扩张上存在区别, MIKC-type主要来源于基因组水平的复制事件, M-type基因扩张主要来自基因组内小范围的复制事件(Edger and Pires, 2009).我们对拟南芥和甘蓝型油菜MADS-box基因进行共线性统计, 发现多数MADS-box基因在甘蓝型油菜中拥有多个拷贝, 其中MIKC-type基因的平均拷贝数约为M-type的2倍.MIKC-type和M-type选择压力的平均值也显示, MIKC- type受到的选择压力更大.这表明基因组复制事件对MIKC-type的扩张起重要作用, 在进化的过程中MIKC-type基因被有选择地保留(Maere et al., 2005). ...
1 1990
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2015
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2014
... 在植物中, MADS-box是一个庞大的转录调控因子家族, 参与许多生长发育的重要过程.例如, 花的形成、开花、果实膨大及衰老等(Alvarez-Buylla et al., 2000a; Theissen et al., 2000; Fang and Fernandez, 2002).植物MADS-box转录因子的发现源于对拟南芥花器官分化的研究(Yanofsky et al., 1990).拟南芥花器官分化ABC模型中的大部分基因都属于MADS- box家族的MIKC-type亚家族(Immink et al., 2010).MIKC-type亚家族基因还参与许多生物和非生物胁迫的响应(Gan et al., 2005; Shao et al., 2010; Hem- ming and Trevaskis, 2011; Yao et al., 2015).在拟南芥中, MIKC-type亚家族基因AGL21调控侧根的生长, 响应环境压力并受到多种植物激素的调控(Yu et al., 2014).水稻(Oryza sativa) MIKC-type亚家族的OsMADS25和OsMADS27参与渗透胁迫响应, OsMADS25、OsMADS27和OsMADS57受硝酸盐诱导表达(Arora et al., 2007).此外, 研究表明MIKC-type亚家族的MIKC*类基因在水稻等单子叶植物花粉发育的晚期起重要作用(Liu et al., 2013).相比于MIKC- type亚家族, 对于M-type基因的研究相对较少.与动物中相比, 植物中M-type基因的产生和丢失远多于动物, 因此早期的研究认为在植物中M-type基因的功能可能没有MIKC-type重要(De Bodt et al., 2003).通过对拟南芥61个M-type基因的组织表达模式进行研究, 发现只有5个基因表达(Kofuji et al., 2003).但近年相继发现M-type基因与植物配子分化、胚和胚乳的发育相关(Day et al., 2008; Tiwari et al., 2010; Wuest et al., 2010; Masiero et al., 2011). ...
1 2006
... 从BRAD网站上下载共线性基因的CDS序列.用MEGA6 (Tamura et al., 2013)内置的Muscle对两物种之间的共线性基因对做codon比对, 然后用KaKs_ Calculator2.0 (Zhang et al., 2006)软件计算共线性基因之间的选择压力. ...
表1 甘蓝型油菜MADS-box基因在亚基因组上的分布 Table 1 Distribution of MADS-box genes in subgenome of Brassica napus
