,2,4,*, 邓书林,2,4,*Genome-wide Identification and Analysis of CONSTANS-like Gene Family in Nicotiana tabacum
Yawen Zhang1,2, Shan Liang1, Guoyun Xu3, Wuxia Guo,2,4,*, Shulin Deng,2,4,*通讯作者: E-mail:guowx@scbg.ac.cn;sldeng@scbg.ac.cn
责任编辑: 朱亚娜
收稿日期:2020-08-25接受日期:2021-01-5网络出版日期:2021-01-01
| 基金资助: |
Corresponding authors: E-mail:guowx@scbg.ac.cn;sldeng@scbg.ac.cn
Received:2020-08-25Accepted:2021-01-5Online:2021-01-01
摘要
烟草(Nicotiana tabacum)是基因功能分析的模式植物以及重要的经济作物之一, 适宜的生存环境对烟草的生长和繁殖至关重要。COL (CONSTANS-like)基因家族编码蛋白不仅调控植物开花, 而且在植物生物/非生物胁迫响应中发挥重要作用。该研究通过鉴定烟草COL基因家族成员, 分析其基因结构、进化关系、转录调控元件和表达模式, 探究其编码蛋白的生物学功能, 尤其是在烟草响应低温胁迫中的可能作用。结果显示, 在烟草中共鉴定出15个COL基因, 其编码的蛋白理化性质相近; 进化分析结果表明其包括3类, 每个类别的成员之间具有相似的外显子/内含子结构以及motif数量和类型; 烟草COL基因启动子区域含有大量与光、低温、干旱以及植物激素等响应相关的顺式作用元件; 基于二代高通量测序分析结果表明, 低温显著影响烟草COL基因的表达, 但对不同基因的影响存在差异, 不同COL基因的亲本(林烟草(N. sylvestris) (母本)和绒毛状烟草(N. tomentosiformis) (父本))具有表达偏好性, 且这种偏好性大部分会从6-7叶期保持到现蕾期。
关键词：
Abstract
Nicotiana tabacum (tobacco) is one of the model plants for molecular biology research as well as an important economic crop in the world. A suitable living environment is essential for the growth and reproduction of tobacco. CONSTANS-like (COL) family proteins are not only key regulators for flowering time, but also play important roles in stress response of plants. Our aim was to identify the COL family members, analyze their gene structure, evolutionary relationship, transcriptional regulatory elements and expression patterns, and explore their possible functions in response to cold stress in tobacco. We identified a total of 15 COL genes with similar physiochemical properties in tobacco. Evolutionary analysis divided all COL genes into three categories, and similar intron structure and motif distribution were observed among genes within each category. The promoter regions of tobacco COL genes contain a large number of cis-acting elements related to responses to light, low temperature, drought and phyto hormone. Gene expression analysis showed that low temperature significantly affected the expression of COL genes in tobacco, but the effects on different genes were different. Our study showed different parental (N. sylvestris (maternal) and N. tomentosiformis (paternal)) expression bias between different COL genes in tobacco, and most of the bias patterns were maintained from 6-7 leaf stage to budding stage.
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引用本文
张雅文, 梁山, 徐国云, 郭无瑕, 邓书林. 烟草CONSTANS-like基因家族的鉴定与分析. 植物学报, 2021, 56(1): 33-43 doi:10.11983/CBB20147
Zhang Yawen, Liang Shan, Xu Guoyun, Guo Wuxia, Deng Shulin.
植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育。由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(Cutler et al., 2010)。在过去几十年中, 人们已经对植物响应环境胁迫(如寒冷、高温、干旱、盐分和洪水)的转录变化进行了广泛研究(Saidi et al., 2011; Miura and Furumoto, 2013; Sauter, 2013; Singh and Laxmi, 2015; Tang et al., 2015; 王玲等, 2017)。
众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(Putterill et al., 1995; Suárez-López et al., 2001)。此外, COL蛋白作为转录因子还与植物形态发育和非生物胁迫响应有关。在拟南芥(Arabidopsis thaliana)中, AtCOL3是光形态发生的正向调节因子, 在COP1 (constitutive photomorphogenic 1)的下游起作用, 同时可以促进根系生长(Datta et al., 2006); AtCOL4通过脱落酸依赖途径正向调控植物的非生物胁迫耐受性(Min et al., 2015); AtCOL7参与光敏色素B (phyB)介导的避光响应, 同时还可以增加拟南芥的分支数(Zhang et al., 2014)。在水稻(Oryza sativa)中, OsCOL9通过水杨酸和乙烯信号转导途径调节水稻对稻瘟病的抗性(Liu et al., 2016a)。Qin等(2018)对棉花(Gossypium hirsutum)的COL基因家族进行分析, 发现来自第2组和第3组的基因可能在应对干旱和盐胁迫中起重要作用。从结构上看, 典型的COL蛋白包含2个保守结构域(Borden, 2000)。其中一个是植物特有的C末端CCT结构域, 主要参与蛋白转录调控以及核蛋白转运(Crocco and Botto, 2013)。另一个是动物中也存在的N端锌指结构(B-box结构域), 在COL蛋白与卷曲螺旋蛋白相互作用过程中发挥重要作用(Holm et al., 2001)。在拟南芥中, 根据B-box结构域的不同, COL蛋白可分为3组。I组包括AtCO和AtCOL1-AtCOL5, 含有2个B-box基序(B-box1 (B1)和B-box2 (B2)); II组包括AtCOL9-AtCOL15, 与I组的蛋白结构相似, 但与B2存在氨基酸序列上的差异; III组包括AtCOL6-AtCOL8和AtCOL16, 只含有1个B-box基序(Griffiths et al., 2003; Khanna et al., 2009)。
普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物。作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(Yamori et al., 2010)。此外, 烟草是在大约20万年前由二倍体林烟草(N. sylvestris) (母本)和绒毛状烟草(N. tomentosiformis) (父本)杂交形成的异源四倍体(Skalická et al., 2005; Leitch et al., 2008)。当2套基因组合并到1个细胞中时, 具有相似或冗余功能基因的重复拷贝可能会改变其基因表达方式, 包括部分同源基因表达偏好、侵略性上调或下调、沉默以及表达时间和位置改变(Doyle et al., 2008; Yoo et al., 2013; Li et al., 2014)。在四倍体棉花(Gossypium spp.)以及六倍体小麦(Triticum aestivum)中均存在部分同源基因表达偏好性现象(Li et al., 2014; Zhang et al., 2015)。因此, 烟草响应低温相关基因的鉴定分析以及同源基因的表达模式研究, 不仅有助于回答生物学领域关于植物胁迫响应机制以及多倍体植物表达调控的基本问题, 而且对于烟草以及其它作物的品质改良具有重要参考价值。
近年来, 虽然已有多种植物COL基因的研究报道, 但关于烟草COL基因功能的报道较少, 尤其是在烟草响应非生物胁迫方面。本研究以烟草基因组数据为基础, 通过生物信息学方法对烟草COL基因家族进行鉴定和分析; 同时结合转录组分析烟草COL基因在不同生长发育阶段以及不同温度处理后的表达情况; 并进一步鉴定出烟草COL基因中的部分同源基因对, 深入研究其亲本表达偏好性以及在不同生长发育阶段和不同温度条件下的表达偏向改变模式, 以期为进一步阐明COL基因家族的功能及其在烟草响应非生物胁迫中的作用机制奠定基础。
1 材料与方法
1.1 实验材料
本研究所用烟草(Nicotiana tabacum L. cv. ‘NC82’)种子由中国农业科学院烟草研究所提供。1.2 烟草COL基因家族的鉴定
从茄科数据库(1.3 COL蛋白进化树的构建
为了构建系统发育树, 我们从NCBI (1.4 COL蛋白理化性质预测
使用Protparam (1.5 COL基因结构及其编码蛋白motif分析
利用在线软件MEME (1.6 COL基因家族启动子的顺式作用元件预测
将烟草所有COL基因的启动子序列(ATG上游2 000 bp)提交到PlantCare网站(1.7 低温处理及取样
取普通烟草品种(NC82)在正常温度条件下(26°C, 光周期为12小时光照/12小时黑暗)进行育苗培养, 幼苗长至6-7叶期时, 将NC82部分植株进行低温处理10天(12°C, 光周期为12小时光照/12小时黑暗), 剩余植株作为对照继续在原条件下生长同样天数。处理结束时, 同时从低温处理幼苗(cold_S)和非低温处理(对照)幼苗(ck_S)上采集叶片样品。然后, 将低温和对照植株置于正常条件下培养直至现蕾期, 对2组植株进行叶片取样, 即现蕾期的低温处理植株(cold_F)和对照植株(ck_F)。4组样品(每组3次生物学重复, 共12个样品)在取样后立即置于液氮中冷冻, 并于-80°C冰箱中保存, 备用。1.8 低温处理下烟草COL基因的表达分析
分别提取上述样品高质量总RNA, 按照Illumina Hiseq2000测序平台构建RNA-seq测序文库并测序。测序产生的原始reads利用FastQC进行质量评估并通过以下条件进行过滤: (1) 含有接头的reads; (2) 含有未知碱基的reads; (3) 低质量碱基(Q≤20)高于50%的reads。过滤所得的高质量reads通过HISAT2比对到烟草基因组上, 利用FeatureCounts (Liao et al., 2014)计算每个基因的reads数, 然后使用DEGseq2 (Love et al., 2014)进行表达差异分析。从中选取15个烟草COL基因的表达量数据, 用GraphPad Prism软件对烟草COL基因表达数据进行分析, 并绘制相对表达量柱状图。利用同样流程分析前期已发表的烟草4°C低温处理表达数据(Jin et al., 2017)。1.9 实时荧光定量PCR
样品处理同转录组测序样品, 每个处理取3次生物学重复。利用Trizol提取样品总RNA, 采用反转录试剂盒(普洛麦格(北京)生物科技有限公司, Cat No.A2790)合成cDNA, 采用Roche Light Cycler 480实时荧光定量PCR仪进行定量分析。PCR反应程序为: 95°C预变性2分钟; 95°C15秒, 60°C1分钟, 40个循环。使用Microsoft office软件对荧光定量PCR结果进行分析并绘制COL基因相对表达量柱状图, 使用软件附带的t-检验进行差异显著性分析。2 结果与讨论
2.1 烟草COL基因的全基因组鉴定及其编码蛋白的理化性质
通过蛋白结构域分析和隐马尔可夫模型筛选, 在烟草基因组中鉴定出15个COL基因(附录1)。以物种拉丁名首字母为前缀, 并根据拟南芥同源基因命名规则将这些基因进行编号。理化性质(附录2)表明, 烟草COL蛋白的氨基酸数目为336-473个, 分子量在37.4- 52.0 kDa之间, 与拟南芥同源蛋白相似。蛋白理论等电点范围在5.07-7.79之间, 其中14个蛋白的等电点小于7, 显酸性, 只有1个蛋白的等电点大于7, 显碱性。所有烟草COL蛋白的不稳定系数均大于40 (41.76-58.1), 为不稳定蛋白。脂肪族氨基酸指数范围为60.68-70.89, 亲水性的总平均值介于-0.795- -0.301之间, 均表现为亲水性。2.2 烟草COL基因编码蛋白的分类与系统进化关系
采用MEGA7软件中的邻接法对烟草(15个)、拟南芥 (17个)、番茄(11个)、水稻(16个)和玉米(18个)的COL蛋白序列(附录3)进行系统发育树构建。结果(图1)显示, 这5种模式植物的COL家族基因均分布在3个分支上(Group I-III), 并未因物种差异单独聚为几类, 表明烟草与其它物种的COL成员之间具有较近的亲缘关系。在各分支内, 烟草COL优先与番茄COL聚集成一个或多个独立小分支, 可能是由于烟草和番茄同属于茄科, 两者亲缘关系较近, 序列相似性更高。Group I和Group II的分支成员蛋白都含有2个B-box和1个CCT结构域, Group III的分支成员蛋白只含有1个B-box和1个CCT结构域。Group I、Group II和Group III分支下分别包含7、4和4个烟草COL基因, 与其它植物相比各分支下的COL基因并未发生明显扩张或缩减。图1
新窗口打开|下载原图ZIP|生成PPT图15个物种COL蛋白的系统发育树
从NCBI数据库下载烟草(Nitab)、拟南芥(At)、番茄(Solyc)、水稻(Os)和玉米(Zma) COL蛋白序列。采用Clustal软件进行序列比对, 采用邻接法构建系统发育树, bar表示进化距离。
Figure 1Phylogenetic tree of COL proteins from five species
COL protein sequences of Nicotiana tabacum (Nitab), Arabidopsis thaliana (At), Solanum lycopersicum (Solyc), Oryza sativa (Os), and Zea mays (Zma) were downloaded from NCBI database. The phylogenetic tree was constructed by neighbor joining method with Clustal, bar indicated evolutionary distance.
2.3 烟草COL基因的基因结构以及蛋白保守基序
基因结构分析(图2A)表明, 烟草COL基因的外显子数目为2-4个, 其中第1类COL基因含有2-3个外显子; 第2类含有4个外显子; 除了NitabCOL16a基因含有3个外显子之外, 其余第3类COL基因均含有2个外显子。一般情况下, 同一组基因的外显子和内含子数量相近, 表明这些基因具有保守的剪接模式。上述结果表明, 烟草中同一类别的COL基因具有较为保守的剪接模式。利用MEME软件对烟草COL蛋白进行序列比对分析, 共找到10个Motif (图2B), 其中最短的是Motif10, 含有14个氨基酸残基, 最长的是Motif1和Motif2, 都含有50个氨基酸残基(图2C)。总之, 烟草各类别COL成员之间Motif的数量和类型较为相似。在第1类COL中, 所有蛋白都含有Motif1-Motif3以及Motif10。在第2类COL中, 除NitabCOL10不含Motif3外, 所有蛋白都含有Motif1-Motif3。在第3类COL中, 所有蛋白都含有Motif1、2、5、7、8, NitabCOL16c和NitabCOL16d还含有Motif6。Motif1 (位于蛋白的C端)和Motif2 (位于蛋白的N端)在所有烟草COL蛋白序列中最为保守, 其次为Motif3, 鉴于此我们将Motif1- 3的序列在Pfam网站进行比对, 结果表明其为CCT结构域和B-box基序。图2
新窗口打开|下载原图ZIP|生成PPT图2烟草COL的基因结构(A)、COL蛋白的保守结构域(B)及蛋白保守基序的氨基酸序列(C)
不同颜色的矩形代表不同的蛋白保守基序以及非编码区(UTR) (绿色)和编码序列(CDS) (黄色)。比例尺分别代表基因序列长度(A)和蛋白序列长度(B), 纵坐标数字代表蛋白保守基序中相应氨基酸的频率(C)。
Figure 2Gene structures of COL genes (A), and conserved motifs (B) and amino acid sequences (C) of conserved motifs of COL proteins in tobacco
Differently colored rectangles representing different protein conserved motifs as well as untranslated region (UTR) (green) and coding sequence (CDS) (yellow). Scale bars indicating gene sequence length (A) and protein sequence length (B), respectively, and the ordinate numbers indicating the frequency of corresponding amino acid in the conserved motifs (C).
2.4 烟草COL基因启动子的顺式作用元件
顺式元件与相应的反式调节因子相互作用进而参与基因调控, 分析基因的顺式元件可为研究其表达调控机制提供有价值的信息。对烟草COL基因启动子区域顺式元件鉴定的结果(附录4)表明, 所有15个COL基因启动子中均含有大量的光响应元件, 这一特点与COL作为光周期途径主要调节因子的功能相符; 所有15个COL基因均含有植物激素诱导元件, 其中数量较多的是茉莉酸甲酯、水杨酸、脱落酸、赤霉素以及生长素响应元件, 表明植物激素可能调控烟草COL的表达。此外, 有7个COL基因(NitabCOL02a、02b、04a、05、14、16a、16b)含有低温响应元件, 6个COL基因(NitabCOL04a、04b、04d、13b、16a、16d)含有干旱诱导元件, 4个COL基因(NitabCOL02a、02b、04c、13b)含有防御和胁迫应答元件, 表明烟草COL家族可能响应低温和干旱胁迫, 参与烟草逆境响应。上述结果表明, 烟草COL基因的表达可能受到光、植物激素及逆境胁迫等多种生理和环境因素调控。2.5 烟草COL蛋白及其亲本的进化关系
为了探究异源四倍体烟草的COL基因家族及其亲本之间的进化关系, 我们在其父本绒毛状烟草和母本林烟草基因组中分别鉴定出13个和9个COL基因, 并构建系统进化树(图3)。结果显示, 有8个烟草COL基因(NitabCOL02a、04a、04d、10、13b、16a、16b、16c)来自父本, 7个烟草COL基因(NitabCOL02b、04b、04c、05、13a、14、16d)来自母本。其中, 有10个烟草COL基因组成了5对部分同源基因, 分别为NitabCOL02a-NitabCOL02b、NitabCOL04a-NitabCOL04b、NitabCOL04c-NitabCOL04d、NitabCOL13a-NitabCOL13b和NitabCOL16c-NitabCOL16d。在剩余的烟草COL基因中, NitabCOL16a和NitabCOL16b均来源于父本, 本研究中未发现来自母本的部分同源基因; 而NitabCOL05来自母本, 没有找到来自于父本的部分同源基因, 这可能是由于它们的相应部分同源基因在四倍体烟草基因组进化过程中丢失所致。此外, 与NitabCOL10聚为一支的多个父本COL基因(Nito09a-d)可能是相应父本基因在进化过程中发生基因重复产生的旁系同源基因。图3
新窗口打开|下载原图ZIP|生成PPT图3烟草及其亲本COL蛋白的系统发育树
从茄科基因组数据库(Solgenomics.net)下载普通烟草(Nitab) (子代)、绒毛状烟草(Nito) (父本)、林烟草(Nisy) (母本) COL蛋白序列, 采用Clustal软件进行序列比对, 并用邻接法构建系统发育树。
Figure 3Phylogenetic tree of the COL family proteins in tobacco and its parents
The COL proteins of Nicotiana tabacum (Nitab) (progeny), N. tomentosiformis (Nito) (paternal), and N. sylvestris (Nisy) (maternal) were downloaded from Solgenomics.net. The phylogenetic tree was constructed by neighbor joining method with Clustal.
2.6 烟草COL基因和部分同源基因在不同生长发育阶段的表达变化以及低温诱导表达
低温影响烟草的生长发育以及烟叶的产量和质量, 在春季过早移栽容易受到低温伤害(樊希彬等, 2016)。为了研究低温对烟草不同生长发育阶段COL基因表达量的影响, 我们对在正常温度以及12°C低温处理下6-7叶期和现蕾期的烟草COL基因的表达量进行了比较分析。结果(图4A)显示, 低温处理后, 有2个基因(NitabCOL02a、05)的表达量无论是在6-7叶期还是现蕾期均不发生变化; 有5个基因(NitabCOL02b、13a、13b、14、16b)在6-7叶期表达量上升, 现蕾期表达量不变; 其余8个基因(NitabCOL04a、04b、04c、04d、10、16a、16c、16d)在6-7叶期表达量下降, 现蕾期表达量不变。同时, 我们选取4个烟草COL基因进行qRT-PCR验证, 与转录组测序结果一致, 即烟草在6-7叶期经历低温后, NitabCOL05表达量不变, NitabCOL13a和NitabCOL14表达量显著上升, NitabCOL16a表达量显著下降(附录5), 表明转录组数据可信。此外, 我们还对K326和CB1的6-7叶期烟草进行4°C低温处理1天, 将其与正常温度下COL基因的表达量进行比较(附录6), 结果表明, 其表达倍数变化与12°C低温处理下6-7叶期烟草(图4A)相比, 正常温度下烟草NitabCOL16c和NitabCOL16d的相对表达量明显更低, NitabCOL13b的相对表达量更高, 即4°C处理条件下, 这三个基因的表达倍数变化更大, 其余基因的表达情况与12°C低温处理相比无显著差异, 说明这3个基因可能对低温更敏感。以上结果表明, 烟草COL基因的表达可能受低温调控或参与低温胁迫响应, 烟草不同COL基因对低温的响应不同, 暗示这些基因的功能可能存在差异。图4
新窗口打开|下载原图ZIP|生成PPT图4烟草所有COL基因(A)和5对部分同源基因(B)-(F)在低温处理下不同发育阶段叶片中的表达
FC(S): 12°C处理下6-7叶期的表达差异倍数; FC(F): 12°C处理下现蕾期的表达差异倍数; ck_S: 26°C下6-7叶期烟草; ck_F: 26°C下现蕾期烟草; cold_S: 12°C处理后6-7叶期烟草; cold_F: 12°C处理后现蕾期烟草; 黑色: 来自父本的基因; 灰色: 来自母本的基因。 相对表达水平为3次生物学重复的平均值, 误差线代表标准差, 采用Student’s t-test对部分同源基因对进行差异显著性检验, * P<0.05, ** P<0.01, *** P<0.001, **** P<0.0001, ns表示无显著性差异。
Figure 4Expression of all COL genes (A) and five homologous genes pairs (B)-(F) in tobacco leaves at different developmental stages under cold treatment
FC(S): Fold change at 6-7 leaf stage under 12°C treatment; FC(F): Fold change at budding stage under 12°C treatment; ck_S: 6-7 leaf stage under 26°C; ck_F: Budding stage under 26°C; cold_S: 6-7 leaf stage under 12°C treatment; cold_F: Budding stage under 12°C treatment; Black: Orthologs from paternal plant; Gray: Orthologs from maternal plant; the relative expression level is the average of 3 biological replicates, the error bar represents standard deviation, and Student’s t-test is used for significance test, * P<0.05, ** P<0.01, *** P<0.001, **** P<0.0001, and ns means not significant.
烟草是一种异源四倍体植物, 理论上, 每个来自父本和母本基因组的基因都会对植株的表型产生影响。为了进一步揭示烟草COL基因的表达模式变化规律与内在机制, 我们对上述从烟草15个COL基因中鉴定出的5对部分同源基因进行了表达偏向性分析。结果(图4B-F)显示, 正常温度条件下, 在6-7叶期所有5对基因都存在显著的亲本表达偏向性, 其中有3对同源基因(NitabCOL04c-NitabCOL04d、NitabCOL13a-NitabCOL13b、NitabCOL16c-NitabCOL16d)偏向母本高表达; 有2对同源基因(NitabCOL02a-NitabCOL02b、NitabCOL04a-NitabCOL04b)偏向父本高表达; 在现蕾期, 大部分同源基因的表达偏向性都与6-7叶期保持一致, 只有1对基因(NitabCOL16c- NitabCOL16d)的母本表达偏向性减弱至不显著。低温处理之后, 在6-7叶期, 有3对基因(NitabCOL02a- NitabCOL02b、NitabCOL04a-NitabCOL04b、NitabCOL13a-NitabCOL13b)的表达偏好性消除, 2对基因(NitabCOL04c-NitabCOL04d、NitabCOL16c-NitabCOL16d)保持与正常温度下的偏好性一致; 在现蕾期, 有2对基因(NitabCOL02a-NitabCOL02b、NitabCOL13a-Nitab-COL13b)的表达偏好性仍然保持消除, 1对基因(NitabCOL16c-NitabCOL16d)保持母本表达偏向, 2对基因(NitabCOL04a-NitabCOL04b、NitabCOL04c-NitabCOL04d)的表达偏好性恢复与正常温度下一致。总之, 在正常温度条件下, 烟草COL基因的亲本表达偏好不同, 且这种偏好性大部分会从6-7叶期保持到现蕾期; 低温处理对这种表达偏向性具有显著影响, 且对不同基因以及在植物不同阶段的影响模式不同。
2.7 讨论
目前已有多种植物COL家族特性和功能的研究报道, 包括模式植物拟南芥和水稻(Griffiths et al., 2003; Khanna et al., 2009)以及非模式植物萝卜(Raphanus sativus) (Hu et al., 2018)等, 但对于烟草这一重要的模式植物和经济作物相关研究仍然十分缺乏。本研究从全基因组水平鉴定出15个烟草COL基因家族成员, 对拟南芥、番茄、玉米、水稻和烟草COL基因家族的系统发育关系进行分析, 发现COL蛋白包括3类, 在每个类别中这5个物种均有涉及(图1)。基因结构分析和结构域分析表明, 同一类别中的COL同源基因之间的外显子/内含子结构相对保守, 结构域相似且高度保守, 而不同类别之间存在显著差异(图2)。整体来看, 烟草COL蛋白既含有共有的保守结构域, 也有各自独特的基序(motif), 烟草COL蛋白中不同基序可能是其功能分化的结构基础。以往的研究表明, CO蛋白不仅与光周期对植物成花的影响密切相关, 而且参与胁迫应答和植物激素信号转导等多种生物学过程。Song等(2008)发现, 拟南芥CO还可以通过与介导水杨酸信号转导的TGA4蛋白互作, 进而调控植物的成花发育。在水稻中, COL基因Ghd2过表达后, 植株对干旱变得敏感, Ghd2可能在加速干旱诱导的水稻叶片衰老中起重要作用(Liu et al., 2016b)。通过启动子分析发现, 烟草COL基因含有大量响应环境因子以及逆境和植物激素的顺式作用元件, 如光反应元件、逆境胁迫(干旱和低温)响应元件、植物激素(茉莉酸甲酯、水杨酸、脱落酸、赤霉素和生长素)以及防御和胁迫应答响应元件, 表明烟草COL基因的表达可能受到光、植物激素和逆境胁迫等多种生理和环境因素的调控(附录4)。烟草不同COL基因启动子区域所含有的特异顺式作用元件的鉴定可为后续深入研究烟草COL基因的生物学功能奠定基础。
与其它二倍体模式植物或作物不同, 烟草是由二倍体亲本杂交产生的异源四倍体, 不同亲本基因组的共存对基因组以及表型相关基因的表达模式具有重要意义(Doyle et al., 2008; Flagel and Wendel, 2010)。鉴别烟草COL基因中来源于不同亲本的部分同源基因是研究其表达调控模式的前提。对林烟草和绒毛状烟草COL基因的鉴定以及与烟草COL基因的系统发育分析表明, 我们所鉴定的15个烟草COL基因中, 8个来自父本绒毛状烟草, 7个来自母本林烟草, 其中10个COL基因组成5对部分同源基因(图3)。少数COL基因没有找到来自父本或母本中的部分同源基因, 这可能是由于烟草的形成已有约20万年, 相应拷贝在进化过程中丢失所致。我们还发现, 烟草个别COL基因(COL10)在父本中存在多个相对应的同源基因, 说明父本中该基因在进化过程中发生了基因扩张。有研究表明, 烟草在多倍化过程中, 其基因组来源于林烟草(S基因组)的比例为53%, 来源于绒毛状烟草(T基因组)的比例为47% (Sierro et al., 2014)。本研究中由于烟草COL基因数目较少, 并未表现出这种比例上的差异。
利用RNA-seq数据进行表达分析, 发现低温处理后, 在烟草6-7叶期, 有2个COL基因的表达量不变, 5个COL基因的表达量上升, 8个COL基因的表达量下降, 所有基因在现蕾期的表达量均不变(图4A), 这与相同条件下部分COL基因的qRT-PCR结果一致。此外, 相比12°C低温处理, 4°C低温处理6-7叶期烟草, NitabCOL16c、NitabCOL16d和NitabCOL13b的相对表达量变化更加明显(附录6), 表明烟草COL基因可能在植物响应低温胁迫过程中发挥重要作用。在烟草6-7叶期, COL基因家族5对部分同源基因中, 有3对偏向母本高表达, 有2对偏向父本高表达, 且大部分基因的表达偏向性持续到现蕾期(图4B-F), 表明在烟草COL基因的表达中, 来自不同亲本的部分同源基因所起的作用和贡献不同。低温处理后, 有2对部分同源基因(NitabCOL02a-NitabCOL02b和NitabCOL13a-NitabCOL13b)的表达偏向性在6-7叶期消除且持续到现蕾期。这种同源基因在响应非生物胁迫后基因表达模式发生改变的现象在其它多倍体植物中也有报道, 可能反映出多倍体植物在进化过程中所形成的应对各种逆境条件的调控方式。例如, 多倍体陆地棉(G. hirsutum)在浸水处理下, AdhA基因的其中一个部分同源基因在下胚轴中沉默; 在低温胁迫处理下, 另一个部分同源基因在下胚轴中沉默(Liu and Adams, 2007)。虽然本研究对烟草各个COL基因的具体功能和调控机制还未深入探究, 但通过在全基因组水平对烟草COL进行基因鉴定、功能预测以及表达模式分析, 可为深入研究COL基因家族在响应非生物胁迫等生物学过程中的作用提供参考。
(责任编辑: 朱亚娜)
附录
附录1 烟草COL基因名称、ID和基本信息Appendix 1 Name, ID and various features of COL genes in Nicotiana tabacum
附录2 烟草COL基因家族及其编码蛋白的理化性质
Appendix 2 Physiochemical properties of the COL gene family and its encoded proteins in tobacco
附录3 烟草、番茄、拟南芥、玉米和水稻COL家族基因成员
Appendix 3 The members of COL gene family identified in Nicotiana tabacum, Solanum lycopersicum, Arabidopsis thaliana, Zea mays and Oryza sativa
附录4 烟草COL基因启动子的顺式作用元件
Appendix 4 Distribution of cis-acting elements in promoter sequences of tobacco COL genes
附录5 实时荧光定量PCR检测低温处理后4个烟草COL基因的相对表达量
Appendix 5 Relative expression of four COL genes in tobacco after low temperature treatment by quantitative RT-PCR
附录6 4°C处理后烟草COL基因的表达热图
Appendix 6 Expression Heatmap of tobacco COL genes under 4°C treatment
Http://www.chinbullbotany.com/fileup/1674-3466/PDF/t20-147.pdf
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The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine (
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The B-box domain is conserved in a large number of proteins involved in cell growth control, differentiation and transcriptional regulation among animal and plant species. In Arabidopsis thaliana, some works have found that B-box proteins (BBX) play central developmental functions in flowering, light and abiotic stress signaling. Despite the functional importance of this protein family, evolutionary and structural relationships of BBX proteins have not been extensively investigated in the plant kingdom. Using a phylogenetic approach, we conducted a comprehensive evolutionary analysis of the BBX protein family in twelve plant species (four green algae, one moss, one lycophyte, three monocots and three dicots). The analysis classified 214 BBX proteins into five structure groups, which evolved independently at early stages of green plant evolution. We showed that the B-box consensus sequences of each structure groups retained a common and conserved domain topology. Furthermore, we identified seven novel motifs specific to each structure group and a valine-proline (VP) pair conserved at the C-terminus domain in some BBX proteins suggesting that they are required for protein-protein interactions. As it has been documented in mammalian systems, we also found monopartite and bipartite amino acid sequences at the C-terminus domain that could function as nuclear localization signals (NLSs). The five BBX structure groups evolved constrained by the conservation of amino acid sequences in the two B-boxes, but radiating variation into NLSs and novel motifs of each structural group. We suggest that these features are the functional basis for the BBX protein diversity in green plants.
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Polyploidy is a common mode of evolution in flowering plants. The profound effects of polyploidy on gene expression appear to be caused more by hybridity than by genome doubling. Epigenetic mechanisms underlying genome-wide changes in expression are as yet poorly understood; only methylation has received much study, and its importance varies among polyploids. Genetic diploidization begins with the earliest responses to genome merger and doubling; less is known about chromosomal diploidization. Polyploidy duplicates every gene in the genome, providing the raw material for divergence or partitioning of function in homoeologous copies. Preferential retention or loss of genes occurs in a wide range of taxa, suggesting that there is an underlying set of principles governing the fates of duplicated genes. Further studies are required for general patterns to be elucidated, involving different plant families, kinds of polyploidy, and polyploids of different ages.
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The CO (CONSTANS) gene of Arabidopsis has an important role in the regulation of flowering by photoperiod. CO is part of a gene family with 17 members that are subdivided into three classes, termed Group I to III here. All members of the family have a CCT (CO, CO-like, TOC1) domain near the carboxy terminus. Group I genes, which include CO, have two zinc finger B-boxes near the amino terminus. Group II genes have one B-box, and Group III genes have one B-box and a second diverged zinc finger. Analysis of rice (Oryza sativa) genomic sequence identified 16 genes (OsA-OsP) that were also divided into these three groups, showing that their evolution predates monocot/dicot divergence. Eight Group I genes (HvCO1-HvCO8) were isolated from barley (Hordeum vulgare), of which two (HvCO1 and HvCO2) were highly CO like. HvCO3 and its rice counterpart (OsB) had one B-box that was distantly related to Group II genes and was probably derived by internal deletion of a two B-box Group I gene. Sequence homology and comparative mapping showed that HvCO1 was the counterpart of OsA (Hd1), a major determinant of photoperiod sensitivity in rice. Major genes determining photoperiod response have been mapped in barley and wheat (Triticum aestivum), but none corresponded to CO-like genes. Thus, selection for variation in photoperiod response has affected different genes in rice and temperate cereals. The peptides of HvCO1, HvCO2 (barley), and Hd1 (rice) show significant structural differences from CO, particularly amino acid changes that are predicted to abolish B-box2 function, suggesting an evolutionary trend toward a one-B-box structure in the most CO-like cereal genes.
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BACKGROUND: CB-1 and K326 are closely related tobacco cultivars; however, their cold tolerance capacities are different. K326 is much more cold tolerant than CB-1. RESULTS: We studied the transcriptomes and metabolomes of CB-1 and K326 leaf samples treated with cold stress. Totally, we have identified 14,590 differentially expressed genes (DEGs) in CB-1 and 14,605 DEGs in K326; there was also 200 differentially expressed metabolites in CB-1 and 194 in K326. Moreover, there were many overlapping genes (around 50%) that were cold-responsive in both plant cultivars, although there were also many differences in the cold responsive genes between the two cultivars. Importantly, for most of the overlapping cold responsive genes, the extent of the changes in expression were typically much more pronounced in K326 than in CB-1, which may help explain the superior cold tolerance of K326. Similar results were found in the metabolome analysis, particularly with the analysis of primary metabolites, including amino acids, organic acids, and sugars. The large number of specific responsive genes and metabolites highlight the complex regulatory mechanisms associated with cold stress in tobacco. In addition, our work implies that the energy metabolism and hormones may function distinctly between CB-1 and K326. CONCLUSIONS: Differences in gene expression and metabolite levels following cold stress treatment seem likely to have contributed to the observed difference in the cold tolerance phenotype of these two tobacco cultivars.
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BACKGROUND: In studies looking at individual polyploid species, the most common patterns of genomic change are that either genome size in the polyploid is additive (i.e. the sum of parental genome donors) or there is evidence of genome downsizing. Reports showing an increase in genome size are rare. In a large-scale analysis of 3008 species, genome downsizing was shown to be a widespread biological response to polyploidy. Polyploidy in the genus Nicotiana (Solanaceae) is common with approx. 40 % of the approx. 75 species being allotetraploid. Recent advances in understanding phylogenetic relationships of Nicotiana species and dating polyploid formation enable a temporal dimension to be added to the analysis of genome size evolution in these polyploids. METHODS: Genome sizes were measured in 18 species of Nicotiana (nine diploids and nine polyploids) ranging in age from <200,000 years to approx. 4.5 Myr old, to determine the direction and extent of genome size change following polyploidy. These data were combined with data from genomic in situ hybridization and increasing amounts of information on sequence composition in Nicotiana to provide insights into the molecular basis of genome size changes. KEY RESULTS AND CONCLUSIONS: By comparing the expected genome size of the polyploid (based on summing the genome size of species identified as either a parent or most closely related to the diploid progenitors) with the observed genome size, four polyploids showed genome downsizing and five showed increases. There was no discernable pattern in the direction of genome size change with age of polyploids, although with increasing age the amount of genome size change increased. In older polyploids (approx. 4.5 million years old) the increase in genome size was associated with loss of detectable genomic in situ hybridization signal, whereas some hybridization signal was still detected in species exhibiting genome downsizing. The possible significance of these results is discussed.
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URLPMID:27829023 [本文引用: 1]
DOI:10.1093/jxb/erw344URLPMID:27638689 [本文引用: 1]
CONSTANS (CO)-like genes have been intensively investigated for their roles in the regulation of photoperiodic flowering, but very limited information has been reported on their functions in other biological processes. Here, we found that a CO-like gene, Ghd2 (Grain number, plant height, and heading date2), which can increase the yield potential under normal growth condition just like its homologue Ghd7, is involved in the regulation of leaf senescence and drought resistance. Ghd2 is expressed mainly in the rice (Oryza sativa) leaf with the highest level detected at the grain-filling stage, and it is down-regulated by drought stress conditions. Overexpression of Ghd2 resulted in significantly reduced drought resistance, while its knockout mutant showed the opposite phenotype. The earlier senescence symptoms and the transcript up-regulation of many senescence-associated genes (SAGs) in Ghd2-overexpressing transgenic rice plants under drought stress conditions indicate that Ghd2 plays essential roles in accelerating drought-induced leaf senescence in rice. Moreover, developmental and dark-induced leaf senescence was accelerated in the Ghd2-overexpressing rice and delayed in the ghd2 mutant. Several SAGs were confirmed to be regulated by Ghd2 using a transient expression system in rice protoplasts. Ghd2 interacted with several regulatory proteins, including OsARID3, OsPURalpha, and three 14-3-3 proteins. OsARID3 and OsPURalpha showed expression patterns similar to Ghd2 in rice leaves, with the highest levels at the grain-filling stage, whereas OsARID3 and the 14-3-3 genes responded differently to drought stress conditions. These results indicate that Ghd2 functions as a regulator by integrating environmental signals with the senescence process into a developmental programme through interaction with different proteins.
[本文引用: 1]
URLPMID:25516281 [本文引用: 1]
DOI:10.1111/jipb.12246URLPMID:25073793 [本文引用: 1]
The precise roles of the B-box zinc finger family of transcription factors in plant stress are poorly understood. Functional analysis was performed on AtCOL4, an Arabidopsis thaliana L. CONSTANS-like 4 protein that is a putative novel transcription factor, and which contains a predicted transcriptional activation domain. Analyses of an AtCOL4 promoter-beta-glucuronidase (GUS) construct revealed substantial GUS activity in whole seedlings. The expression of AtCOL4 was strongly induced by abscisic acid (ABA), salt, and osmotic stress. Mutation in atcol4 resulted in increased sensitivity to ABA and salt stress during seed germination and the cotyledon greening process. In contrast, AtCOL4-overexpressing plants were less sensitive to ABA and salt stress compared to the wild type. Interestingly, in the presence of ABA or salt stress, the transcript levels of other ABA biosynthesis and stress-related genes were enhanced induction in AtCOL4-overexpressing and WT plants, rather than in the atcol4 mutant. Thus, AtCOL4 is involved in ABA and salt stress response through the ABA-dependent signaling pathway. Taken together, these findings provide compelling evidence that AtCOL4 is an important regulator for plant tolerance to abiotic stress.
DOI:10.3390/ijms14035312URLPMID:23466881 [本文引用: 1]
Plants are constantly exposed to a variety of environmental stresses. Freezing or extremely low temperature constitutes a key factor influencing plant growth, development and crop productivity. Plants have evolved a mechanism to enhance tolerance to freezing during exposure to periods of low, but non-freezing temperatures. This phenomenon is called cold acclimation. During cold acclimation, plants develop several mechanisms to minimize potential damages caused by low temperature. Cold response is highly complex process that involves an array of physiological and biochemical modifications. Furthermore, alterations of the expression patterns of many genes, proteins and metabolites in response to cold stress have been reported. Recent studies demonstrate that post-transcriptional and post-translational regulations play a role in the regulation of cold signaling. In this review article, recent advances in cold stress signaling and tolerance are highlighted.
DOI:10.1016/0092-8674(95)90288-0URLPMID:7697715 [本文引用: 1]
The vegetative and reproductive (flowering) phases of Arabidopsis development are clearly separated. The onset of flowering is promoted by long photoperiods, but the constans (co) mutant flowers later than wild type under these conditions. The CO gene was isolated, and two zinc fingers that show a similar spacing of cysteines, but little direct homology, to members of the GATA1 family were identified in the amino acid sequence. co mutations were shown to affect amino acids that are conserved in both fingers. Some transgenic plants containing extra copies of CO flowered earlier than wild type, suggesting that CO activity is limiting on flowering time. Double mutants were constructed containing co and mutations affecting gibberellic acid responses, meristem identity, or phytochrome function, and their phenotypes suggested a model for the role of CO in promoting flowering.
[本文引用: 1]
[本文引用: 1]
DOI:10.1038/ncomms4833URLPMID:24807620 [本文引用: 1]
The allotetraploid plant Nicotiana tabacum (common tobacco) is a major crop species and a model organism, for which only very fragmented genomic sequences are currently available. Here we report high-quality draft genomes for three main tobacco varieties. These genomes show both the low divergence of tobacco from its ancestors and microsynteny with other Solanaceae species. We identify over 90,000 gene models and determine the ancestral origin of tobacco mosaic virus and potyvirus disease resistance in tobacco. We anticipate that the draft genomes will strengthen the use of N. tabacum as a versatile model organism for functional genomics and biotechnology applications.
DOI:10.3389/fpls.2015.00895URLPMID:26579147 [本文引用: 1]
Drought is one of the leading factors responsible for the reduction in crop yield worldwide. Due to climate change, in future, more areas are going to be affected by drought and for prolonged periods. Therefore, understanding the mechanisms underlying the drought response is one of the major scientific concerns for improving crop yield. Plants deploy diverse strategies and mechanisms to respond and tolerate drought stress. Expression of numerous genes is modulated in different plants under drought stress that help them to optimize their growth and development. Plant hormone abscisic acid (ABA) plays a major role in plant response and tolerance by regulating the expression of many genes under drought stress. Transcription factors being the major regulator of gene expression play a crucial role in stress response. ABA regulates the expression of most of the target genes through ABA-responsive element (ABRE) binding protein/ABRE binding factor (AREB/ABF) transcription factors. Genes regulated by AREB/ABFs constitute a regulon termed as AREB/ABF regulon. In addition to this, drought responsive genes are also regulated by ABA-independent mechanisms. In ABA-independent regulation, dehydration-responsive element binding protein (DREB), NAM, ATAF, and CUC regulons play an important role by regulating many drought-responsive genes. Apart from these major regulons, MYB/MYC, WRKY, and nuclear factor-Y (NF-Y) transcription factors are also involved in drought response and tolerance. Our understanding about transcriptional regulation of drought is still evolving. Recent reports have suggested the existence of crosstalk between different transcription factors operating under drought stress. In this article, we have reviewed various regulons working under drought stress and their crosstalk with each other.
URLPMID:15760371 [本文引用: 1]
URLPMID:18587275
DOI:10.1038/35074138URLPMID:11323677 [本文引用: 1]
Flowering is often triggered by exposing plants to appropriate day lengths. This response requires an endogenous timer called the circadian clock to measure the duration of the day or night. This timer also controls daily rhythms in gene expression and behavioural patterns such as leaf movements. Several Arabidopsis mutations affect both circadian processes and flowering time; but how the effect of these mutations on the circadian clock is related to their influence on flowering remains unknown. Here we show that expression of CONSTANS (CO), a gene that accelerates flowering in response to long days, is modulated by the circadian clock and day length. Expression of a CO target gene, called FLOWERING LOCUS T (FT), is restricted to a similar time of day as expression of CO. Three mutations that affect circadian rhythms and flowering time alter CO and FT expression in ways that are consistent with their effects on flowering. In addition, the late flowering phenotype of such mutants is corrected by overexpressing CO. Thus, CO acts between the circadian clock and the control of flowering, suggesting mechanisms by which day length regulates flowering time.
DOI:10.3109/07388551.2014.889080URLPMID:24738851 [本文引用: 1]
The increasing seriousness of salinization aggravates the food, population and environmental issues. Ameliorating the salt-resistance of plants especially the crops is the most effective measure to solve the worldwide problem. The salinity can cause damage to plants mainly from two aspects: hyperosmotic and hyperionic stresses leading to the restrain of growth and photosynthesis. To the adverse effects, the plants derive corresponding strategies including: ion regulation and compartmentalization, biosynthesis of compatible solutes, induction of antioxidant enzymes and plant hormones. With the development of molecular biology, our understanding of the molecular and physiology knowledge is becoming clearness. The complex signal transduction underlying the salt resistance is being illuminated brighter and clearer. The SOS pathway is the central of the cell signaling in salt stress. The accumulation of the compatible solutes and the activation of the antioxidant system are the effective measures for plants to enhance the salt resistance. How to make full use of our understanding to improve the output of crops is a huge challenge for us, yet the application of the genetic engineering makes this possible. In this review, we will discuss the influence of the salt stress and the response of the plants in detail expecting to provide a particular account for the plant resistance in molecular, physiological and transgenic fields.
DOI:10.1111/j.1365-3040.2009.02067.xURLPMID:19895395 [本文引用: 1]
Effects of growth light intensity on the temperature dependence of CO(2) assimilation rate were studied in tobacco (Nicotiana tabacum) because growth light intensity alters nitrogen allocation between photosynthetic components. Leaf nitrogen, ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco) and cytochrome f (cyt f) contents increased with increasing growth light intensity, but the cyt f/Rubisco ratio was unaltered. Mesophyll conductance to CO(2) diffusion (g(m)) measured with carbon isotope discrimination increased with growth light intensity but not with measuring light intensity. The responses of CO(2) assimilation rate to chloroplast CO(2) concentration (C(c)) at different light intensities and temperatures were used to estimate the maximum carboxylation rate of Rubisco (V(cmax)) and the chloroplast electron transport rate (J). Maximum electron transport rates were linearly related to cyt f content at any given temperature (e.g. 115 and 179 micromol electrons mol(-1) cyt f s(-1) at 25 and 40 degrees C, respectively). The chloroplast CO(2) concentration (C(trans)) at which the transition from RuBP carboxylation to RuBP regeneration limitation occurred increased with leaf temperature and was independent of growth light intensity, consistent with the constant ratio of cyt f/Rubisco. In tobacco, CO(2) assimilation rate at 380 micromol mol(-1) CO(2) concentration and high light was limited by RuBP carboxylation above 32 degrees C and by RuBP regeneration below 32 degrees C.
DOI:10.1038/hdy.2012.94URLPMID:23169565 [本文引用: 1]
Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we explored gene expression patterns in interspecific hybrid F(1), and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up- or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F(1) hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection.
DOI:10.1038/nbt.3207URLPMID:25893781 [本文引用: 1]
Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
DOI:10.1093/mp/ssu058URLPMID:24908267 [本文引用: 1]
Arabidopsis phytochrome B (phyB) is the major photoreceptor that senses the ratio of red to far-red light (R:FR) to regulate the shade-avoidance response (SAR). It has been hypothesized that altered homeostasis of phytohormones such as auxin and strigolactone is at least partially responsible for SAR, but the mechanism underlying phyB regulation of the hormonal change is not fully understood. Previously we reported that CONSTANS-LIKE 7 (COL7) enhances branching number under high R:FR but not under low R:FR, implying that COL7 may be involved in the phyB-mediated SAR. In this study, we provide evidence that COL7 reduces auxin levels in a high R:FR-dependent manner. We found that the phyB mutation suppresses the COL7-induced branching proliferation. Moreover, COL7 promotes mRNA expression of SUPERROOT 2 (SUR2), which encodes a suppressor of auxin biosynthesis, in high R:FR but not in low R:FR. Consistently with these results, deficiency of phyB suppresses the elevated transcription of SUR2 in COL7 overexpression plants grown in high R:FR. Taking these results together with data suggesting that photo-excited phyB is required for stabilization of the COL7 protein, we argue that COL7 is a critical factor linking light perception to changes in auxin level in Arabidopsis.
气候条件对烟草生长的影响分析
1
2016
... 低温影响烟草的生长发育以及烟叶的产量和质量, 在春季过早移栽容易受到低温伤害(
水稻非生物胁迫响应基因OsMIP1的表达与进化分析
1
2017
... 植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育.由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(
RING domains: master builders of molecular scaffolds?
1
2000
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
TBtools: an integrative toolkit developed for interactive analyses of big biological data
1
2020
... 利用在线软件MEME (
BBX proteins in green plants: insights into their evolution, structure, feature and functional diversification
1
2013
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
Abscisic acid: emergence of a core signaling network
1
2010
... 植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育.由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(
Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth
1
2006
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
Evolutionary genetics of genome merger and doubling in plants
2
2008
... 普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物.作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(
... 与其它二倍体模式植物或作物不同, 烟草是由二倍体亲本杂交产生的异源四倍体, 不同亲本基因组的共存对基因组以及表型相关基因的表达模式具有重要意义(
Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation
1
2010
... 与其它二倍体模式植物或作物不同, 烟草是由二倍体亲本杂交产生的异源四倍体, 不同亲本基因组的共存对基因组以及表型相关基因的表达模式具有重要意义(
The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis
2
2003
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
... 目前已有多种植物COL家族特性和功能的研究报道, 包括模式植物拟南芥和水稻(
Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1
1
2001
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus)
2
2018
... 为了构建系统发育树, 我们从NCBI (
... 目前已有多种植物COL家族特性和功能的研究报道, 包括模式植物拟南芥和水稻(
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
1
2017
... 分别提取上述样品高质量总RNA, 按照Illumina Hiseq2000测序平台构建RNA-seq测序文库并测序.测序产生的原始reads利用FastQC进行质量评估并通过以下条件进行过滤: (1) 含有接头的reads; (2) 含有未知碱基的reads; (3) 低质量碱基(Q≤20)高于50%的reads.过滤所得的高质量reads通过HISAT2比对到烟草基因组上, 利用FeatureCounts (
The Arabidopsis B-box zinc finger family
2
2009
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
... 目前已有多种植物COL家族特性和功能的研究报道, 包括模式植物拟南芥和水稻(
The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae)
1
2008
... 普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物.作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(
mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat
2
2014
... 普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物.作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(
... )中均存在部分同源基因表达偏好性现象(
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
1
2014
... 分别提取上述样品高质量总RNA, 按照Illumina Hiseq2000测序平台构建RNA-seq测序文库并测序.测序产生的原始reads利用FastQC进行质量评估并通过以下条件进行过滤: (1) 含有接头的reads; (2) 含有未知碱基的reads; (3) 低质量碱基(Q≤20)高于50%的reads.过滤所得的高质量reads通过HISAT2比对到烟草基因组上, 利用FeatureCounts (
CONSTANS-Like 9 (OsCOL9) interacts with receptor for activated C-Kinase 1 (OsRACK1) to regulate blast resistance through salicylic acid and ethylene signaling pathways
1
2016
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
Ghd2, a CONSTANS-like gene, confers drought sensitivity through regulation of senescence in rice
1
2016
... 以往的研究表明, CO蛋白不仅与光周期对植物成花的影响密切相关, 而且参与胁迫应答和植物激素信号转导等多种生物学过程.Song等(2008)发现, 拟南芥CO还可以通过与介导水杨酸信号转导的TGA4蛋白互作, 进而调控植物的成花发育.在水稻中, COL基因Ghd2过表达后, 植株对干旱变得敏感, Ghd2可能在加速干旱诱导的水稻叶片衰老中起重要作用(
Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development
1
2007
... 利用RNA-seq数据进行表达分析, 发现低温处理后, 在烟草6-7叶期, 有2个COL基因的表达量不变, 5个COL基因的表达量上升, 8个COL基因的表达量下降, 所有基因在现蕾期的表达量均不变(
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
1
2014
... 分别提取上述样品高质量总RNA, 按照Illumina Hiseq2000测序平台构建RNA-seq测序文库并测序.测序产生的原始reads利用FastQC进行质量评估并通过以下条件进行过滤: (1) 含有接头的reads; (2) 含有未知碱基的reads; (3) 低质量碱基(Q≤20)高于50%的reads.过滤所得的高质量reads通过HISAT2比对到烟草基因组上, 利用FeatureCounts (
The CONSTANS-like 4 transcription factor, AtCOL4, positively regulates abiotic stress tolerance through an abscisic acid-dependent manner in Arabidopsis
1
2015
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
Cold signaling and cold response in plants
1
2013
... 植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育.由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(
The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors
1
1995
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
Genome-wide analysis elucidates the role of CONSTANS- like genes in stress responses of cotton
0
2018
Heat perception and signaling in plants: a tortuous path to thermotolerance
1
2011
... 植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育.由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(
Root responses to flooding
1
2013
... 植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育.由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(
The tobacco genome sequence and its comparison with those of tomato and potato
1
2014
... 与其它二倍体模式植物或作物不同, 烟草是由二倍体亲本杂交产生的异源四倍体, 不同亲本基因组的共存对基因组以及表型相关基因的表达模式具有重要意义(
Transcriptional regulation of drought response: a tortuous network of transcriptional factors
1
2015
... 植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育.由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(
Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco
1
2005
... 普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物.作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(
Isolation of CONSTANS as a TGA4/OBF4 interacting protein
0
2008
CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis
1
2001
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
Global plant-responding mechanisms to salt stress: physiological and molecular levels and implications in biotechnology
1
2015
... 植物在其生命周期中需经历不断变化的环境, 昼夜和季节变化带来的温度差异、光照、降雨和养分供应情况均影响植物的生长发育.由于植物不能移动, 因此进化出了灵活的信号响应网络, 使其能够快速重新调整自身发育、生理和新陈代谢, 以应对环境胁迫(
Effects of growth and measurement light intensities on temperature dependence of CO2 assimilation rate in tobacco leaves
1
2010
... 普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物.作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(
Homoeolog expression bias and expression level dominance in allopolyploid cotton
1
2013
... 普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物.作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
1
2015
... 普通烟草(Nicotiana tabacum) (以下简称烟草)不仅是基因功能研究的主要模式植物之一, 也是全世界广泛种植的以叶片为主要收获对象的重要经济作物.作为起源于热带地区的嗜热作物, 烟草对温度变化敏感, 在温带的早春季节发生的短暂低温也会影响植物叶片的生长(
CONSTANS-LIKE 7 (COL7) is involved in phytochrome B (phyB)-mediated light-quality regulation of auxin homeostasis
1
2014
... 众所周知, COL (CONSTANS-like)基因家族中的CO是光周期途径中的关键基因, 通过光周期途径整合昼夜节律、光信号以及分生组织相关基因来调节开花时间, 在调控植物开花过程中发挥重要作用(
