彭威^,, 冯蒙洁, 陈皓, 韩宝瑜^,中国计量大学,浙江省生物计量及检验检疫技术重点实验室,杭州 310018

Progress on genome sequencing of Dipteran insects

Wei Peng^,, Mengjie Feng, Hao Chen, Baoyu Han^,Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China

通讯作者: *彭威。韩宝瑜,博士,教授,研究方向：昆虫化学生态学。E-mail:hanby15@163.com

编委: 张蔚
收稿日期:2020-05-6修回日期:2020-09-6网络出版日期:2020-11-20

基金资助:

联合国粮农组织和国际原子能署项目编号.D44003 国家重点研发计划项目编号.2018YFC1604402 浙江省重点研发计划项目编号.2020C02026 浙江省基础公益研究计划项目资助编号.LGN18C160006 浙江省基础公益研究计划项目资助编号.LGN20C140005

Received:2020-05-6Revised:2020-09-6Online:2020-11-20

Fund supported:

Supported by the International Atomic Energy Agency’s Coordinated Research Project No.D44003 the National Key Research and Development Program of China No.2018YFC1604402 the Key Research and Development Program of Zhejiang Province, China No.2020C02026 the Fundamental and Public Welfare of Zhejiang Province of China Nos.LGN18C160006 the Fundamental and Public Welfare of Zhejiang Province of China Nos.LGN20C140005

作者简介 About authors
彭威,博士,讲师,研究方向：昆虫生物化学与分子生物学。E-mail:E-mail：pengwei@cjlu.edu.cn。






摘要
双翅目(Diptera)是完全变态昆虫中种类最多样化的昆虫,也是第一个基因组已完整测序的昆虫。目前共有110种双翅目昆虫具有公开的基因组,其中黑腹果蝇(Drosophila melanogaster)和冈比亚按蚊(Anopheles gambiae)包含数百个种群基因组。比较基因组学阐明了双翅目昆虫的多种生物学问题,为基因组结构变异、遗传机制以及基因、物种、种群的进化速率和进化模式的研究提供了新思路。尽管双翅目昆虫基因组资源丰富,但仍有许多物种缺乏基因组信息。双翅目昆虫基因组研究对于揭示吸血、寄生、授粉和噬菌性等重要行为的多重起源具有重要价值。本文主要介绍了双翅目昆虫基因组的分布和不同物种基因组的特性,以及双翅目昆虫基因组中功能基因如细胞色素P450、免疫、性别决定和分化相关基因的研究进展,对双翅目昆虫比较基因组学中的重大发现进行了总结,以期在快速发展的基因组组学时代为其他物种进行基因组测序提供指导和借鉴,为开发基于基因组的害虫防治和治理提供理论基础。
关键词： 双翅目昆虫;基因组特性;功能基因;比较基因组学;系统进化

Abstract
Diptera is among the most diverse holometabolan insect orders and was the earliest order to have a genome fully sequenced. The genomes of 110 fly species have been sequenced and published and many hundreds of population- level genomes have been obtained in the model organisms Drosophila melanogaster and Anopheles gambiae. Comparative genomics elucidate many aspects of the Dipteran biology, thereby providing insights for on the variability in genome structure, genetic mechanisms, and rates and patterns of evolution in genes, species, and populations. Despite the availability of genomic resources in Diptera, there is still a significant lack of information on many other insects. The sequencing of the genomes in Dipteran insects would be of great value to exhibit multiple origins of key fly behaviors such as blood feeding, parasitism, pollination, and mycophagy. In this review, we briefly summarize the distribution and characteristics of Dipteran genomes, introduce the progress of functional genes such as Cytochrome P450, immunity, sex determination and differentiation related genes in Dipteran genome, and highlight the significant findings generated by comparative genomics approach among Dipteran species. This paper provides the guidelines and references for choosing additional taxa for genome sequencing studies in the rapidly developing genome omics era, and offers a fundamental basis for genome-based pest control and management.
Keywords：Diptera;genome characteristics;functional genes;comparative genomics;phyletic evolution


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本文引用格式
彭威, 冯蒙洁, 陈皓, 韩宝瑜. 双翅目昆虫基因组研究进展. 遗传[J], 2020, 42(11): 1093-1109 doi:10.16288/j.yczz.20-130
Wei Peng. Progress on genome sequencing of Dipteran insects. Hereditas(Beijing)[J], 2020, 42(11): 1093-1109 doi:10.16288/j.yczz.20-130


昆虫是动物界种类最丰富的古老类群。目前地球上已知的昆虫有100万种左右,估计全世界昆虫总数在1000万种以上。其中,双翅目(Diptera)昆虫分布广、数量大、种类多样化,大约包含180个属,总计158,000个种,分为5个主要的下目,即大蚊下目(Tipulomorpha)、蚊下目(Culicomorpha)、蛾蚋下目(Psychodomorpha)、毛蚊下目(Bibionomorpha)和短角下目(Brachycera)^[1,2,3]。短角下目包括约20个总科,总计80,000个物种。其中包括起源于1.8亿年前的短角亚目(Lower Brachycera)和起源于0.65亿年前的环裂亚目(Cyclorrhapha)。环裂亚目超过78个科,习性多样,包括植食性、寄生性、食真菌、哺乳动物寄生性、蛆病、吸血以及幼虫取食腐烂有机质的腐食性。另外,重要的传粉昆虫如食蚜蝇科(Syrphidae)和蜂虻科(Bombyliidae)也主要分布在环裂亚目。在传粉昆虫和开花植物互作中,适应和提高传粉的能力是双翅目昆虫形态多样性、物种多样性和生态多样性的重要驱动力^[4,5,6]。双翅目既包括造成巨大生产损失的农业害虫如地中海实蝇(Ceratitis capitata)、麦瘿蚊(Mayetiola destructor)和丝光绿蝇(Lucilia sericata),又包括危害健康的卫生害虫如家蝇(Musca domestica)、埃及伊蚊(Aedes aegypti)和冈比亚按蚊(Anopheles gambiae)。其中蚊虫叮咬传播的疾病每年可导致200万人死亡。双翅目昆虫中也有为农业生态系统中的开花植物提供授粉的传粉昆虫如食蚜蝇科和蜂虻科。双翅目昆虫生活史、行为习性、取食习性和形态适应性具有多样性^[1]。

模式物种黑腹果蝇(Drosophila melanogaster),媒介昆虫如埃及伊蚊、冈比亚按蚊和采采蝇(Glossina morsitans),农业害虫如地中海实蝇、麦瘿蚊和丝光绿蝇是双翅目昆虫中早期完成基因组完整测序的物种。同时,非模式物种基因组测序物种的数量也在增加^[7,8]。目前双翅目昆虫中有多达110个物种已完成且可公开获取完整的基因组序列信息(http://i5k.github.io/arthropod_genomes_at_ncbi)。双翅目昆虫基因组测序数量的稳步增长、以及系统发育基因组学和比较基因组学的发展为研究种间和种内水平的昆虫遗传机制和进化过程提供了新的视角。双翅目昆虫基因组测序样本覆盖率的增加为评估果蝇属和蚊子外物种进化提供了极为重要的参考。双翅目昆虫种间和种内的系统发育基因组学和比较基因组学已经在基因调控和修复^[9,10,11,12]、发育^[13,14]、神经生物学^[15,16]、性别决定^[17]、昆虫抗药性^[18,19]、营养专化^[20]和生态适应^[21,22,23]等方面产生了重大的研究成果。毫无疑问,通过下一代基因测序技术和更加完善的基因组数据库,双翅目昆虫基因组研究将推动昆虫基因组学的发展,从系统生物学的角度来解决昆虫学研究中的问题,为农业害虫和病媒昆虫绿色防控提供新策略。本文综述了双翅目昆虫基因组在不同物种中的分布和研究现状,介绍了双翅目昆虫基因组的特性和双翅目昆虫基因组中功能基因如细胞色素P450、免疫、性别决定和分化相关基因研究进展,总结了双翅目昆虫比较基因组学中的重大发现,以期为了解双翅目昆虫多样性、生物学特性以及基于基因组的害虫防治和治理提供参考。

1 双翅目基因组研究现状

分子进化、系统发育和化石等证据将双翅目昆虫的起源定于2.6亿年前的二叠纪晚期,大约与其

他主要的全变态昆虫同时开始出现^[2,24]。由于双翅目物种间巨大的形态差异、遗传多样性和快速进化的历史进程,对充分阐明双翅目昆虫生命进化构成了挑战。但是系统进化基因组学研究有助于促进我们对双翅目生命进化的理解^[1,25]。目前,双翅目亚目已完成110个物种基因组测序,主要分布在蚊科和果蝇科(表1)。(1)蚊科：按蚊科共完成27个物种基因组测序,鉴定了冈比亚按蚊吸血生理适应性和免疫相关基因表达,为了解吸血性媒介昆虫的生理适应机制及疟疾的发病机理提供了理论依据^[26];发现致倦库蚊(Culex quinquefasciatus)嗅觉和味觉受体、唾液腺基因和杀虫剂解毒作用相关基因家族数目增加^[27];分析了Anopheles punctulatus基因漂流和种群历史演变^[28];利用Hi-C技术更新了埃及伊蚊基因组染色体读长^[29];利用长读长测序方法对白纹伊蚊(Aedes albopictus)基因组重测序,发现其N50>3 Mb^[30];对16种按蚊科蚊虫的基因组比较鉴定出基因倒置和参与病媒竞争基因的快速进化^[31]。(2)果蝇科：共完成33个物种基因组测序,主要是Brachycera、Cyclorrhapha、Schizophora、Ephydroidea。其中分析了黑腹果蝇基因组结构,其2/3为常染色质,1/3为异染色质,异染色质主要包括简单重复序列、中度重复元件和一些单拷贝DNA,鉴定了与DNA复制、染色体行为、转录和基因调控等相关的蛋白家族^{[32,33,34,35,36,37]};研究了Drosophila pseudoobscura染色体倒置现象^[38];对12种果蝇D. melanogaster、D. pseudoobscura、Drosophila sechellia、Drosophila simulans、Drosophila yakuba、Drosophila erecta、Drosophila ananassae、Drosophila persimilis、Drosophila willistoni、Drosophila mojavensis、Drosophila virilis和Drosophila grimshawi基因组测序比较分析,发现其在基因组大小、基因数量、转座子分布等方面表现出高度保守性,与环境互作和生殖相关蛋白编码基因、非编码RNA、顺式调节区出现变异^[39]。对变色伏绕眼果蝇(Phortica variegata)等10中果蝇性染色体差异的进化模式进行了研究,发现不同果蝇间性染色体组型存在极大地差异性^[7,25]。

随着高通量测序技术的发展,越来越多的非模式双翅目昆虫基因组信息得以公布^[40,41,42]。已完成的医学或农业重要性物种的基因组测序可为广大科研工作者探索潜在的害虫防控机制提供重要参考。双翅目农业重要性物种基因组测序包括多种作物或果蔬害虫,如小麦害虫麦瘿蝇和10种实蝇科(Tephritidae)害虫,如地中海实蝇、橄榄果实蝇(Bactrocera oleae)。另外,丽蝇科如丝光绿蝇和铜绿蝇(Lucilia cuprina)是绵羊蝇蛆病的重要载体,其基因组测序工作具有极其重要的价值^[43]。地中海实蝇基因组鉴定超过1800个与入侵和寄主适应相关基因家族发生扩张^[44];瓜实蝇(Zeugodacus cucurbitae)基因组筛选出多个用于害虫防治研究的候选靶标基因;鉴定了防治铜绿蝇的靶标基因^[43];麦瘿蚊基因组鉴定出426个效应家族基因和2个抵御寄主植物抗性基因^[45]。双翅目医学重要性物种基因组测序包括多种吸血媒介昆虫的基因组,如沙蝇3个毛蠓科(Psychodidae)物种、采采蝇6个舌蝇科(Glossinidae)物种和螯蝇1个蝇科(Muscidae)物种;鉴定了摇蚊科Chironomus tentans唾液腺相关基因表达和Clunio marinus蛋白激酶相关基因表达^[46,47];伏蝇(Phormia regina)基因组可以应用于法医鉴定^[48];舌蝇科总共完成6个物种基因组测序,鉴定了Glossinidae morsitans泌乳特异蛋白和卵胎生发育过程^[49];家蝇科中家蝇基因组基因拷贝数增加,免疫系统识别和效应基因多样^[19],厩螫蝇(Stomoxys calcitrans)基因组主要用于采采蝇基因组的比较分析;蚤蝇科蛆症异蚤蝇(Megaselia scalaris)基因组起初被用作低覆盖率基因组分析检测^[50];由于难以获取足够高质量长须罗蛉(Lutzomyia longipalpis)和巴氏白蛉(Phlebotomus papatasi)DNA,导致毛蠓科基因组测序困难。最近完成超过35个物种基因组测序工作显著提高了双翅目昆虫非模式物种测序覆盖率和基因组学及性染色体差异的进化模式研究,包括潜蝇科班潜蝇(Liriomyza trifolii)、食虫虻科Holcocephala fusca、丽蝇科红头丽蝇(Calliphora vicina)和丝光绿蝇、萤蚊科Chaoborus trivitattus和Mochlonyx cinctipes、摇蚊科Chironomus riparius、突眼蝇科Sphyracephala brevicornis和Teleopsis dalmanni、长足蝇科Condylostylus patibulatus、果蝇科Phortica variegata和Scaptodrosophila lebanonesis、实蝇科橄榄果实蝇等^[7,8](表1)。

Table 1
表1
表1双翅目昆虫基因组信息汇总
Table 1The Summary of Dipteran genome assemblies

科名	物种名	基因组序列号	基因组 大小(Mb)	Contig N50 (bp)	特点	参考文献
潜蝇科 (Agromyzidae)	Liriomyza trifolii	GCA_001014935.1	69.70	1816	班潜蝇性染色体差异的进化模式研究	[7]
食虫虻科 (Asilidae)	Holcocephala fusca	GCA_001015215.1	516.23	1778	性染色体差异的进化模式研究	[7]
	Proctacanthus coquilletti	GCA_001932985.1	208.91	781,095	基因组杂合性为0.47%,重复序列 为15%	[8]
丽蝇科 (Calliphoridae)	Calliphora vicina	GCA_001017275.1	459.23	1086	红头丽蝇性染色体差异的进化模式 研究	[7]
	Lucilia sericata	GCA_001014835.1	319.94	1613	丝光绿蝇性染色体差异的进化模式 研究	[7]
	Phormia regina	GCA_001735545.1	549.93	5563	伏蝇的法医鉴定	[48]
	Lucilia cuprina	GCA_000699065.2	378.27	94,823	鉴定防治铜绿蝇靶标基因	[43]
瘿蚊科 (Cecidomyiidae)	Mayetiola destructor	GCA_000149185.1	185.83	14,032	麦瘿蚊基因组鉴定出426个效应家族基因和2个抵御寄主植物抗性基因	[45]
萤蚊科 (Chaoboridae)	Chaoborus trivitattus	GCA_001014815.1	269.28	2040	性染色体差异的进化模式研究	[7]
	Mochlonyx cinctipes	GCA_001014845.1	441.26	3304	性染色体差异的进化模式研究	[7]
摇蚊科 (Chironomidae)	Belgica antarctica	GCA_000775305.1	89.58	13,687	南极蠓是双翅目昆虫基因组基因数量最少的	[51]
	Chironomus riparius	GCA_001014505.1	154.53	7097	性染色体差异的进化模式研究	[7]
	Chironomus tentans	GCA_000786525.1	213.46	7697	鉴定了唾液腺相关基因表达	[46]
	Clunio marinus	GCA_900005825.1	85.49	154,800	鉴定了蛋白激酶相关基因表达	[47]
按蚊科 (Culicidae, 共完成27个 物种基因组测序)	Aedes aegypti	GCA_009613055.1	1,278.73	11,757,361	利用Hi-C技术更新了埃及伊蚊 染色体读长	[29]
	Aedes albopictus	GCA_006496715.1	2,538.37	1,184,735	利用长片段进行白纹伊蚊基因组 重测序,其N50 > 3 Mbp	[30]
	Culex quinquefasciatus	GCA_000209185.1	579.04	28,546	致倦库蚊嗅觉和味觉受体、唾液腺 基因和杀虫剂解毒作用相关基因家 族数目增加	[27]
	Anopheles gambiae	GCA_001542645.1	250.72	101,465	鉴定了冈比亚按蚊吸血生理适应性 相关基因表达	[26]
	Anopheles punctulatus	GCA_000956255.1	146.16	10,256	分析了基因漂流和种群历史演变	[28]
突眼蝇科 (Diopsidae)	Sphyracephala brevicornis	GCA_001015235.1	315.52	1477	性染色体差异的进化模式研究	[7]
	Teleopsis dalmanni	GCA_002237135.1	545.60	64,047	性染色体差异的进化模式研究	[7]
长足蝇科 (Dolichopodidae)	Condylostylus patibulatus	GCA_001014875.1	451.94	1110	性染色体差异的进化模式研究	[7]
水蝇科 (Ephydridae)	Cirrula hians	GCA_001015075.1	399.69	1781	性染色体差异的进化模式研究	[7]
	Ephydra gracilis	GCA_001014675.1	410.87	2117	性染色体差异的进化模式研究	[7]
舌蝇科 (Glossinidae, 共完成6个物种 基因组测序)	Glossinidae morsitans	GCA_001077435.1	363.11	49,769	鉴定了泌乳特异蛋白和卵胎生 发育过程	[49]
蝇科 (Muscidae)	Musca domestica	GCF_000371365.1	750.4	11,807	家蝇基因拷贝数增加,免疫系统 识别和效应基因多样	[19]
	Stomoxys calcitrans	GCF_001015335.1	971.19	11,309	厩螫蝇基因组主要用于采采蝇 基因组的比较分析
	Haematobia irritans	GCA_003123925.1	1,143.54	5359	性染色体差异的进化模式研究	[7]
蚤蝇科 (Phoridae)	Megaselia abdita	GCA_001015175.1	412.27	3270	性染色体差异的进化模式研究	[7]
	Megaselia scalaris	GCA_000341915.2	488.10	931	蛆症异蚤蝇基因组起初被用作 低覆盖率基因组分析检测	[50]
毛蠓科 (Psychodidae)	Clogmia albipunctata	GCA_001014945.1	256.25	9,372	性染色体差异的进化模式研究	[7]
	Lutzomyia longipalpis	GCA_000265325.1	154.23	7,481	由于难以获取足够高质量长须罗蛉DNA,导致其基因组测序困难
	Phlebotomus papatasi	GCA_000262795.1	363.77	5795	由于难以获取足够高质量巴氏白蛉DNA,导致其基因组测序困难
麻蝇科 (Sarcophagidae)	Neobellieria bullata	GCA_001017455.1	476.29	1894	性染色体差异的进化模式研究	[7]
	Sarcophagidae sp. BV-2014	GCA_001047195.1	494.58	1035	性染色体差异的进化模式研究	[7]
粪蚊科 (Scatopsidae)	Coboldia fuscipes	GCA_001014335.1	98.76	145,453	性染色体差异的进化模式研究	[7]
鼓翅绳科 (Sepsidae)	Themira minor	GCA_001014575.1	99.89	2825	性染色体差异的进化模式研究	[7]
水虻科 (Stratiomyidae)	Hermetia illucens	GCA_009835165.1	1,101.33	258,950	性染色体差异的进化模式研究	[7]
食蚜蝇科 (Syrphidae)	Eristalis dimidiata	GCA_001015145.1	315.43	405	性染色体差异的进化模式研究	[7]
实蝇科 (Tephritidae, 共完成10个 物种基因组测序)	Ceratitis capitata	GCA_000347755.4	436.48	845,931	地中海实蝇基因组鉴定超过1800个与入侵和寄主适应相关mRNA出现基因扩张	[44]
	Bactrocera oleae	GCA_001188975.4	403.08	187,710	性染色体差异的进化模式研究	[7]
	Eutreta diana	GCA_001015115.1	233.05	387	性染色体差异的进化模式研究	[7]
	Tephritis californica	GCA_001017515.1	342.26	906	性染色体差异的进化模式研究	[7]
	Trupanea jonesi	GCA_001014665.1	97.28	865	性染色体差异的进化模式研究	[7]
	Zeugodacus cucurbitae	GCA_000806345.1	374.81	17,360	瓜实蝇基因组主要用于害虫防治研究
大蚊科 (Tipulidae)	Tipula oleracea	GCA_001017535.1	541.7	600	性染色体差异的进化模式研究	[7]
毫蚊科 (Trichoceridae)	Trichoceridae sp. BV-2014	GCA_001014425.1	41.57	1395	性染色体差异的进化模式研究	[7]

新窗口打开|下载CSV

2 双翅目昆虫基因组特性

双翅目昆虫基因组测序始于环裂亚目的黑腹果蝇^[32]和蚊下目的冈比亚按蚊^[26]和埃及伊蚊^[52]。黑腹果蝇、冈比亚按蚊和埃及伊蚊基因组的完成不仅催生了基因组数据库、注释参考文库以及生物信息学分析的成功建立和发展,而且极大地推动了国际合作组织对12种果蝇属和16种按蚊属双翅目昆虫的基因组测序和组装工作^[31,39]。果蝇科种群基因组计划(Drosophila population genomics project, DPGP)已收录超过1121种果蝇科野生种群基因组序列^[38]。果蝇基因参考图谱(Drosophila genetic reference panel, DPGP)包含205种黑腹果蝇品系全基因组关联分析(genome-wide association study, GWAS)数据^[53,54,55]。因此,双翅目昆虫基因组的差异性主要来自蚊子和果蝇这两个分化水平显著不同的分支。蚊子和果蝇是双翅目现存世系中最古老的两个分支,其共同的祖先来自大约2.4亿年前^[2]。果蝇属物种分支进化跨度最近为24万年前,最远为2200万年前至5500万年前之间^[56];按蚊属物种分支进化跨度最近为54万年前,最远为180万年前至1亿年前之间^[57]。蚊子与果蝇间、双翅目其他昆虫间以及双翅目与其他目昆虫间的比较基因组学揭示了双翅目昆虫基因组进化速率显著加快^[58],使得双翅目昆虫相对于其他昆虫而言是名副其实的“长枝”进化物种。而蚊子和果蝇的比较基因组学表明这两类昆虫以显著较大的速率从彼此分化出去,进而进化为双翅目中两大类^[59,60]。

双翅目昆虫基因组大小差异巨大,从毫蚊科Trichoceridae sp. BV-2014的41.57 Mb到白纹伊蚊的2538.37 Mb不等(表1)。即使在同一个科中,基因组的大小也差异很大,按蚊科基因组大小从146.16~ 2538.37 Mb,而果蝇科基因组大小变化相对较小,从117~386 Mb^[61]。双翅目昆虫基因组大小差异巨大的原因可能是其转座子(TEs)和其他重复非编码DNA的差异导致^[62,63]。TEs不仅介导物种的进化和新基因的形成,而且参与基因组的表观调控以及异染色质结构的形成。双翅目昆虫基因组中存在的大量非编码DNA是产生遗传变异的重要来源,影响基因组大小的进化方向。双翅目昆虫基因组包含的基因数量差异很大。黑腹果蝇基因组总共有13,920个基因,致倦库蚊基因组总共有18,955个基因。双翅目昆虫基因组基因数量最少的是南极蠓(Belgica antarctica)中的13,517个^[51],最多的是家蝇中的23,884个^[64]。南极蠓是南极大陆上唯一一种真正意义上的昆虫,也是南极大陆特有的物种。测序发现其基因组规模高度简化,大约只包含9900万个碱基对,基因组中重复的基因序列很少,但与代谢功能、生长发育相关的基因却足够多。南极蠓在漫长的进化过程中,通过剔除非必须基因序列不断调整遗传信息从而适应严酷环境。这为研究生物在极端环境下的进化方向等提供了重要参考^[51]。家蝇以人类和动物的排泄物为生,是包括肺结核、伤寒等多种疾病的载体。基因组测序分析发现家蝇基因组多样性高,存在大量与免疫相关基因和特殊的解毒基因,揭示了家蝇对人类疾病产生免疫力和分解废弃物的机制,这为害虫综合防治、废弃物的分解利用和人类疾病的治疗提供了一定的线索和思路^[19]。地中海实蝇是一种毁灭性的果蔬害虫,现已分布于80多个国家和地区,危害包括柑桔、苹果、梨等水果和蔬菜在内的250多种寄主,其基因组大小为479 Mb,基因组注释获得14,547个基因,有1608个进化的新基因。黑腹果蝇、家蝇和地中海实蝇基因组比较分析,发现地中海实蝇多个基因、基因家族出现扩张现象,这可能是导致地中海实蝇具有较高的适应性和入侵性的原因^[44]。

3 双翅目昆虫基因组中功能基因研究进展

3.1 细胞色素P450基因

P450酶系包括多功能氧化酶和细胞色素P450 (CYP450)单加氧酶。其功能高度多样,包括合成昆虫发育和繁殖所需的重要激素和化学代谢物质,从而促进昆虫对寄主植物的适应性和对环境中有毒物质如杀虫剂的解毒作用。黑腹果蝇细胞色素P450家族共鉴定出90个基因,分属25个家族,其中CYP4和CYP6家族的成员最多,占P450基因总数的一半^[32]。地中海实蝇细胞色素P450家族包含103个基因和9个假基因,相较于黑腹果蝇的88个CYP450基因和3个假基因,地中海实蝇细胞色素P450家族显著扩张,主要集中于CYP6和CYP12基因家族,其扩张性却低于家蝇CYP6和CYP12基因家族^[44]。地中海实蝇CYP6家族由40个基因和4个假基因组成,是黑腹果蝇CYP6家族23个基因的几乎两倍。其中CYP6A、CYP6G和CYP6D亚家族出现显著扩张,CYP6A包含14个基因、CYP6G包含9个基因、CYP6D包含5个基因^[44]。这3个亚家族基因和双翅目昆虫杀虫剂抗性相关,其中CYP6A家族通过基因簇复制快速扩张^[65]。另外,在地中海实蝇基因组中发现18个连续的CYP基因形成一个基因簇(13个属于CYP6A亚家族),其中CYP6A51基因的过表达和氯氟氰菊酯抗性相关^[66]。在黑腹果蝇基因组中发现2个和9个连续的CYP6基因形成两个基因簇。地中海实蝇CYP12基因家族出现复制表明其参与环境响应如细胞色素P450调控的抗性。家蝇和黑腹果蝇CYP12基因家族和杀虫剂抗性相关^[65]。此外,细胞色素P450家族还包含蜕皮激素合成途径相关基因,在地中海实蝇基因组中发现4个P450基因phantom (CYP306A1)、disembodied (CYP302A1)、shadow (CYP315A1)、shade (CYP314A1)能够活化蜕皮激素。

3.2 免疫相关基因

免疫反应包括黑化作用、吞噬作用、包埋、凝血和脂肪体合成抗菌肽和抗菌蛋白^[67]。涉及病菌识别和防御反应的四条主要信号途径是：Toll、IMD、JAK/STAT和JNK^[68]。昆虫主要通过模式识别受体(PRRs)和肽聚糖识别蛋白(PGRPs)家族基因识别细菌,革兰氏阴性细菌结合蛋白(GNBPs)通过结合细菌配体从而激活免疫途径^[69,70,71]。黑腹果蝇基因组鉴定出379个假定的免疫基因,地中海实蝇基因组鉴定出413个假定的免疫基因,家蝇基因组鉴定出771个假定的免疫基因。家蝇基因组中免疫基因数量巨大、免疫识别和受体基因的拷贝数和基因多样性显著增加的原因可能和其生活在富含病原菌的环境相关^[19]。家蝇免疫识别受体Nimrods和thioester- containing proteins (Teps)拷贝数出现显著扩张。家蝇具有17个Nimrods蛋白、19个Teps蛋白。黑腹果蝇具有11个Nimrods蛋白、6个Teps蛋白。在已测序果蝇属物种中,Nimrods基因家族的拷贝数差异较大^[72]。由于地中海实蝇极其多样的寄主选择性导致其免疫基因数量较多,从而应对寄主和环境条件中多种多样的病原菌^[44]。革兰氏阴性细菌和真菌诱导免疫响应因子sp?tzle基因激活Toll信号途径,地中海实蝇由于在不同果实上产卵接触到的真菌感染导致sp?tzle家族基因和Toll受体家族基因出现高度扩张。地中海实蝇有17个Toll受体家族基因,而黑腹果蝇和家蝇只有9个。sp?tzle基因活化所必需的丝氨酸蛋白酶基因家族在地中海实蝇中也出现显著扩张,相较于黑腹果蝇的45个和家蝇的28个,地中海实蝇具有50个丝氨酸蛋白酶基因^[44]。

3.3 性别决定和分化相关基因

地中海实蝇基因组已鉴定出35个直接或者间接参与性别决定和性别分化基因,其中25个基因包括transformer (tra)、doublesex (dsx)、Sexl-lethal (Sxl)基因,6个性别特异剪切基因和4个基因具有躯体性别特异功能如剂量补偿^[44,73,74]。通过比较家蝇雌成虫和雄成虫基因的表达量,已鉴定出113个雄性偏向性表达基因和81个雌性偏向性表达基因^[19]。而在黑腹果蝇中10%~20%的基因具有性别偏向性表达的特性,比家蝇观察到的明显增多^[75,76]。近年来双翅目昆虫基因组测序很大一部分是关于性染色体差异的进化模式研究(表1),而基于基因组测序的策略已鉴定出多种雄性性别决定因子。埃及伊蚊染色体性别决定系统缺少Y染色体,Hall等^[77]基于雌雄基因组测序发现埃及伊蚊雄性决定因子Nix基因位于1号染色体的非重组区域,处于性别决定级联反应的顶端,通过调控下游dsx基因mRNA前体雄性特异剪切和表达,促进雄性发育。Krzywinska等^[78]对冈比亚按蚊雌雄胚胎基因序列比较,在Y染色体上鉴定出一个仅在雄性早期转录表达Yob基因,发现Yob调控dsx基因的雄性特异剪切和表达,从而实现雄性发育。家蝇有一个与众不同的多态性别决定系统,雄性携带一个显性的雄性决定因子,这个因子可以位于X或者Y或者任意5条常染色体上。基于家蝇基因组序列信息,Sharma等^[79]阐明其性别决定系统由雄性决定因子male determiner (Mdmd)的存在与否来决定。Meccariello等^[80]通过对地中海实蝇雄虫构建长读长基因组文库,筛选出性别决定基本信号是位于Y染色体上的雄性决定因子Maleness- on the-Y (MoY)基因,MoY通过阻止合子中tra基因活化,导致tra基因进行雄性特异剪切,引起雄性发育。此外,MoY基因作为雄性决定因子在双翅目实蝇科其他物种如橄榄果实蝇和橘小实蝇(Bactrocera dorsalis)中也是Y染色体连接,且功能保守^[80]。

4 双翅目昆虫比较基因组学研究进展

目前,基因组结构、基因含量、共线性、染色体倒位和非编码元件进化研究是比较基因组学研究的重要领域^[39,81,82]。双翅目昆虫比较基因组学研究阐明了新基因的形成^[83,84]、基因和基因组互作与调控^[85]和基因组塑造昆虫生物史^[86,87]等分子生物学问题。利用种属水平的系统发育比较基因组学,双翅目昆虫中基因家族的进化关系逐渐得到阐述。家蝇作为世界性的卫生害虫,由于其独特的取食习性、长期暴露在杀虫剂下以及与动物病原菌之间的互作,系统发育比较基因组学已证明其与生理和行为适应性相关的细胞色素P450基因家族、化学感受受体和气味结合蛋白基因的拷贝数发生了显著变化^[57]。已有研究表明,按蚊属基因组基因拷贝数的扩增和收缩比果蝇属快5倍^[19]。蚊科和果蝇科中数量巨大的高质量基因组数据可用于小型调控元件如microRNA、piwi-interacting RNA、Aubergine和功能性小阅读框(smORF)的鉴定和系统进化分析^{[88,89,90,91]}。

双翅目昆虫比较基因组学为阐明昆虫进化模式和机制、适应性和生理功能以及基因型和表型之间的联系提供了一个很好的手段。通过比较冈比亚按蚊不同染色体间的系统进化分析模式,发现其基因组中存在大量基因渗入现象,这为解释新形成物种之间常染色体至X染色体的基因转移速率差异提供了新的证据^[57]。比较基因组学为计算近缘物种种群动态、种群分类排序和基因渗入在塑造昆虫遗传差异性等方面提供一个完整的研究系统^[92]。蚊子间比较基因组学对于了解病原菌传播的基本生物学过程以及探索调控病媒昆虫防治的遗传机制具有越来越重要的价值^[93,94]。根据果蝇科已测序基因组建立的系统发育进化树已被用来研究种间基因、基因组、调控网络、发育途径和生态适应等分子生物学问题的进化框架^[95,96]。目前,总共有30种果蝇科昆虫完成基因组组装,其中23种来自水果果蝇亚属(Sophophora subgenus),另外7种来自果蝇亚属(Drosophila subgenus)。果蝇科昆虫间的比较基因组学有助于阐明DNA结合蛋白的基因调控机制,并鉴定出塑造双翅目发育、行为和生理过程的保守直系同源调控基因结构^[97,98]。

双翅目昆虫功能基因组学和比较基因组学是研究昆虫与植物互作的重要手段。植物寄生性麦廮蝇的基因组研究表明,有多种基因产物充当效应蛋白抑制植物防御,并调节宿主细胞诱导植物产生五倍子^[45]。地中海实蝇功能基因组学鉴定出多种气味结合蛋白、水通道蛋白和免疫反应基因,参与调控宿主植物适应性协同进化^[44]。果蝇科昆虫在发育进程中的植食性已出现多次进化,对斑翅果蝇(Drosophila suzukii)和黄果蝇(Scaptomyza flava)的比较基因组学研究发现,取食受损植物组织和取食正常植物组织前后会导致基因表达出现显著性变化,主要包括与营养、规避植物防御和寄主定位相关基因的表达^[99,100,101]。鉴于双翅目昆虫测序成本相对较低,大量果蝇科和蚊子种群基因组测序工作得以完成。果蝇科种群基因组计划和果蝇基因参考图谱是研究定量遗传学的重要参考文库,可获得和测定特定品系的定量表型,并可鉴定其与先前基因组序列的关联性^[53,54,55]。利用DPGP已实现果蝇科昆虫48种定量表型的遗传学分析^[42]。此外,双翅目昆虫具有高丰度和高耐受的染色体内倒位现象,拟暗果蝇(Drosophila pseudoobscura) 54个种群基因组学研究对3号染色体倒位多态性进行了鉴定^[38]。对分布在非洲的765种冈比亚按蚊和Anopheles coluzzii个体进行测序发现,相较于黑腹果蝇0.5%的个体多态性和人类0.5%个体多态性,蚊子个体多态性为3%^[102]。冈比亚按蚊种群基因组测序不仅推动了某些假定基因驱动(gene drive)的应用,还鉴定出远距离基因漂流现象和物种间基因渗入与抗性等位基因的传播有关。

5 结语与展望

目前虽然有大量双翅目昆虫完成基因组测序工作,但是测序样本范围极度失衡,已有基因组主要集中在果蝇科和蚊科,双翅目其它科物种基因组测序还比较缺乏,许多常见科中的昆虫尚未进行测序^[103]。首先,通过实验室饲养、区域生物调查合作和全球基因组计划等可以实现双翅目昆虫基因组测序样本的多样化。双翅目中取食习性和行为习性多样的物种或者模式物种可继续充当未来基因组测序工作的主要对象。眼蕈蚊(Sciaridae)就是其中一个很好的候选对象：多数眼蕈蚊是腐生或以真菌为食,但少数也能侵入活体植物组织。因而眼蕈蚊是研究发育调控基因扩增、性别决定、细胞凋亡、免疫以及染色体结构多态性遗传机制的模式物种^[104]。对双翅目昆虫生理、生态或行为特征具有差异性的近缘物种进行基因组测序,能有效阐明昆虫生物适应的遗传和分子机制。其次,食蚜蝇科(Syrphidae)、蚤蝇科(Phoridae)、秆蝇科(Chloropidae)和家蝇科(Muscidae)昆虫有植食性、寄生性和食真菌性等多种食性,而丽蝇科(Calliphoridae)、麻蝇科(Sarcophagidae)、家蝇科(Muscidae)、虱蝇科(Hippoboscidae)和狂蝇科(Oestridae)昆虫具有哺乳动物或鸟类寄生性和无脊椎动物寄生性等。这些昆虫的比较基因组学研究将有助于阐明双翅目昆虫适应性的关键遗传调控因子。而对双翅目中医学重要性物种进行基因组测序将有助于揭示吸血和栖息地习性转变等一系列行为的遗传学基础。蚋科(Simuliidae)昆虫刺吸人畜的血液,是人畜蟠尾丝虫病的传播媒介,然而蚋科尚无完整的基因组序列信息。最后,寄生昆虫、传粉昆虫和捕食昆虫基因组信息也极其缺乏。栖息地或寄主选择具有差异性的物种间的比较基因组学研究将揭示双翅目昆虫寄主专化性、寄主寻找和规避寄主免疫系统的协同进化模式。将来对双翅目更多科昆虫进行基因组测序是了解双翅目昆虫基因和基因组,以及基因组功能如性染色体进化和多样性的重要手段^[33]。因此,全基因组测序、功能基因组学、进化生物学、比较基因组学、生物信息学分析等技术是推动双翅目昆虫基因组学在害虫防治、资源昆虫利用、药物靶点开发及进化生物学等方面应用的重要手段^{[105,106,107,108,109]}。

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[68] Boutros M, Agaisse H, Perrimon N . Sequential activation of signaling pathways during innate immune responses in Drosophila
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[69] Kang DW, Liu G, Lundstr?m A, Gelius E, Steiner H . A peptidoglycan recognition protein in innate immunity conserved from insects to humans
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[70] Kim YS, Ryu JH, Han SJ, Choi KH, Nam KB, Jang IH, Lemaitre B, Breyi PT, Lee WJ . Gram-negative bacteria-binding protein, a pattern recognition receptor for lipopolysaccharide and β-1,3-glucan that mediates the signaling for the induction of innate immune genes inDrosophila melanogaster cells
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Pattern recognition receptors, non-clonal immune proteins recognizing common microbial components, are critical for non-self recognition and the subsequent induction of Rel/NF-kappaB-controlled innate immune genes. However, the molecular identities of such receptors are still obscure. Here, we present data showing that Drosophila possesses at least three cDNAs encoding members of the Gram-negative bacteria-binding protein (DGNBP) family, one of which, DGNBP-1, has been characterized. Western blot, flow cytometric, and confocal laser microscopic analyses demonstrate that DGNBP-1 exists in both a soluble and a glycosylphosphatidylinositol-anchored membrane form in culture medium supernatant and on Drosophila immunocompetent cells, respectively. DGNBP-1 has a high affinity to microbial immune elicitors such as lipopolysaccharide (LPS) and beta-1,3-glucan whereas no binding affinity is detected with peptidoglycan, beta-1,4-glucan, or chitin. Importantly, the overexpression of DGNBP-1 in Drosophila immunocompetent cells enhances LPS- and beta-1,3-glucan-induced innate immune gene (NF-kappaB-dependent antimicrobial peptide gene) expression, which can be specifically blocked by pretreatment with anti-DGNBP-1 antibody. These results suggest that DGNBP-1 functions as a pattern recognition receptor for LPS from Gram-negative bacteria and beta-1, 3-glucan from fungi and plays an important role in non-self recognition and the subsequent immune signal transmission for the induction of antimicrobial peptide genes in the Drosophila innate immune system.

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[73] Gomulski LM, Dimopoulos G, Xi ZY, Soares MB, Bonaldo MF, Malacrida AR, Gasperi G . Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata
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[74] Gabrieli P, Falaguerra A, Siciliano P, Gomulski LM, Scolari F, Zacharopoulou A, Franz G, Malacrida AR, Gasperi G . Sex and the single embryo: early deveopment in the Mediterranean fruit fly, Ceratitis capitata
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[75] Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B . Constraint and turnover in sex-biased gene expression in the genus Drosophila
Nature, 2007,450(7167):233-237.
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Both genome content and deployment contribute to phenotypic differences between species. Sex is the most important difference between individuals in a species and has long been posited to be rapidly evolving. Indeed, in the Drosophila genus, traits such as sperm length, genitalia, and gonad size are the most obvious differences between species. Comparative analysis of sex-biased expression should deepen our understanding of the relationship between genome content and deployment during evolution. Using existing and newly assembled genomes, we designed species-specific microarrays to examine sex-biased expression of orthologues and species-restricted genes in D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis and D. mojavensis. We show that averaged sex-biased expression changes accumulate monotonically over time within the genus. However, different genes contribute to expression variance within species groups compared to between groups. We observed greater turnover of species-restricted genes with male-biased expression, indicating that gene formation and extinction may play a significant part in species differences. Genes with male-biased expression also show the greatest expression and DNA sequence divergence. This higher divergence and turnover of genes with male-biased expression may be due to high transcription rates in the male germline, greater functional pleiotropy of genes expressed in females, and/or sexual competition.

[76] Gnad F, Parsch J . Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression
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[77] Hall AB, Basu S, Jiang XF, Qi YM, Timoshevskiy VA, Biedler JK, Sharakhova MV, Elahi R, Anderson MA, Chen XG, Sharakhov IV, Adelman ZN, Tu ZJ . A male-determining factor in the mosquito Aedes aegypti
Science, 2015,348(6240):1268-1270.
DOI:10.1126/science.aaa2850URLPMID:25999371 [本文引用: 1]
Sex determination in the mosquito Aedes aegypti is governed by a dominant male-determining factor (M factor) located within a Y chromosome-like region called the M locus. Here, we show that an M-locus gene, Nix, functions as an M factor in A. aegypti. Nix exhibits persistent M linkage and early embryonic expression, two characteristics required of an M factor. Nix knockout with clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 resulted in largely feminized genetic males and the production of female isoforms of two key regulators of sexual differentiation: doublesex and fruitless. Ectopic expression of Nix resulted in genetic females with nearly complete male genitalia. Thus, Nix is both required and sufficient to initiate male development. This study provides a foundation for mosquito control strategies that convert female mosquitoes into harmless males.

[78] Krzywinska E, Dennison NJ, Lycett G, Krzywinski J . A maleness gene in the malaria mosquito Anopheles gambiae
Science, 2016,353(6294):67-69.
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The molecular pathways controlling gender are highly variable and have been identified in only a few nonmammalian model species. In many insects, maleness is conferred by a Y chromosome-linked M factor of unknown nature. We have isolated and characterized a gene, Yob, for the M factor in the malaria mosquito Anopheles gambiae Yob, activated at the beginning of zygotic transcription and expressed throughout a male's life, controls male-specific splicing of the doublesex gene. Silencing embryonic Yob expression is male-lethal, whereas ectopic embryonic delivery of Yob transcripts yields male-only broods. This female-killing property may be an invaluable tool for creation of conditional male-only transgenic Anopheles strains for malaria control programs.

[79] Sharma A, Heinze S, Wu Y, Kohlbrenner T, Morilla I, Brunner C, Wimmer E, van de Zande L, Robinson M, Beukeboom L, Bopp D, . Male sex in houseflies is determined by Mdmd, a paralog of the generic splice factor gene CWC22
Science, 2017,356(6338):642-645.
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[80] Meccariello A, Salvemini M, Primo P, Hall B, Koskinioti P, Dalikova M, Gravina A, Gucciardino MA, Forlenza F, Gregoriou M, Ippolito D, Monti SM, Petrella V, Perrotta MM, Schmeing S, Ruggiero A, Scolari F, Giordano E, Tsoumani KT, Marec F, Windbichler N, Arunkumar KP, Bourtzis K, Mathiopoulos KD, Ragoussis J, Vitagliano L, Tu ZJ, Papathanos PA, Robinson MD, Saccone G . Maleness- on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests
Science, 2019,365(6460):1457-1460.
DOI:10.1126/science.aax1318URLPMID:31467189 [本文引用: 2]
In insects, rapidly evolving primary sex-determining signals are transduced by a conserved regulatory module controlling sexual differentiation. In the agricultural pest Ceratitis capitata (Mediterranean fruit fly, or Medfly), we identified a Y-linked gene, Maleness-on-the-Y (MoY), encoding a small protein that is necessary and sufficient for male development. Silencing or disruption of MoY in XY embryos causes feminization, whereas overexpression of MoY in XX embryos induces masculinization. Crosses between transformed XY females and XX males give rise to males and females, indicating that a Y chromosome can be transmitted by XY females. MoY is Y-linked and functionally conserved in other species of the Tephritidae family, highlighting its potential to serve as a tool for developing more effective control strategies against these major agricultural insect pests.

[81] Von Grotthuss M, Ashburner M, Ranz JM . Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
Genome Res, 2010,20(8):1084-1096.
DOI:10.1101/gr.103713.109URLPMID:20601587 [本文引用: 1]
During evolution, gene repatterning across eukaryotic genomes is not uniform. Some genomic regions exhibit a gene organization conserved phylogenetically, while others are recurrently involved in chromosomal rearrangement, resulting in breakpoint reuse. Both gene order conservation and breakpoint reuse can result from the existence of functional constraints on where chromosomal breakpoints occur or from the existence of regions that are susceptible to breakage. The balance between these two mechanisms is still poorly understood. Drosophila species have very dynamic genomes and, therefore, can be very informative. We compared the gene organization of the main five chromosomal elements (Muller's elements A-E) of nine Drosophila species. Under a parsimonious evolutionary scenario, we estimate that 6116 breakpoints differentiate the gene orders of the species and that breakpoint reuse is associated with approximately 80% of the orthologous landmarks. The comparison of the observed patterns of change in gene organization with those predicted under different simulated modes of evolution shows that fragile regions alone can explain the observed key patterns of Muller's element A (X chromosome) more often than for any other Muller's element. High levels of fragility plus constraints operating on approximately 15% of the genome are sufficient to explain the observed patterns of change and conservation across species. The orthologous landmarks more likely to be under constraint exhibit both a remarkable internal functional heterogeneity and a lack of common functional themes with the exception of the presence of highly conserved noncoding elements. Fragile regions rather than functional constraints have been the main determinant of the evolution of the Drosophila chromosomes.

[82] Jiang Xf, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche YS, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VLM, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi YM, Settlage R, Tojo M, Tubio JMC, Unger MF, Wang B, Vernick KD, Ribeiro JMC, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu ZJ . Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi
Genome Biol, 2014,15(9):459.
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[83] Zhou Q, Zhang GJ, Zhang Y, Xu SY, Zhao RP, Zhan ZB, Li X, Ding Y, Yang S, Wang W . On the origin of new genes in Drosophila
Genome Res, 2008,18(9):1446-1455.
DOI:10.1101/gr.076588.108URLPMID:18550802 [本文引用: 1]
Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole-genome level. Here, we unveil genome-wide patterns for the mutational mechanisms leading to new genes and their subsequent lineage-specific evolution at different time nodes in the Drosophila melanogaster species subgroup. We find that (1) tandem gene duplication has generated approximately 80% of the nascent duplicates that are limited to single species (D. melanogaster or Drosophila yakuba); (2) the most abundant new genes shared by multiple species (44.1%) are dispersed duplicates, and are more likely to be retained and be functional; (3) de novo gene origination from noncoding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes; (4) retroposition is also an important mechanism, and had generated approximately 10% of the new genes; (5) approximately 30% of the new genes in the D. melanogaster species complex recruited various genomic sequences and formed chimeric gene structures, suggesting structure innovation as an important way to help fixation of new genes; and (6) the rate of the origin of new functional genes is estimated to be five to 11 genes per million years in the D. melanogaster subgroup. Finally, we survey gene frequencies among 19 globally derived strains for D. melanogaster-specific new genes and reveal that 44.4% of them show copy number polymorphisms within a population. In conclusion, we provide a panoramic picture for the origin of new genes in Drosophila species.

[84] Zhao L, Saelao P, Jones CD, Begun DJ . Origin and spread of de Novo genes in Drosophila melanogaster populations
Science, 2014,343(6172):769-772.
DOI:10.1126/science.1248286URLPMID:24457212 [本文引用: 1]
Comparative genomic analyses have revealed that genes may arise from ancestrally nongenic sequence. However, the origin and spread of these de novo genes within populations remain obscure. We identified 142 segregating and 106 fixed testis-expressed de novo genes in a population sample of Drosophila melanogaster. These genes appear to derive primarily from ancestral intergenic, unexpressed open reading frames, with natural selection playing a significant role in their spread. These results reveal a heretofore unappreciated dynamism of gene content.

[85] Mackay TFC . Epistasis and quantitative traits: using model organisms to study gene-gene interactions
Nat Rev Genet, 2014,15(1):22-33.
DOI:10.1038/nrg3627URLPMID:24296533 [本文引用: 1]
The role of epistasis in the genetic architecture of quantitative traits is controversial, despite the biological plausibility that nonlinear molecular interactions underpin the genotype-phenotype map. This controversy arises because most genetic variation for quantitative traits is additive. However, additive variance is consistent with pervasive epistasis. In this Review, I discuss experimental designs to detect the contribution of epistasis to quantitative trait phenotypes in model organisms. These studies indicate that epistasis is common, and that additivity can be an emergent property of underlying genetic interaction networks. Epistasis causes hidden quantitative genetic variation in natural populations and could be responsible for the small additive effects, missing heritability and the lack of replication that are typically observed for human complex traits.

[86] Bhutkar A, Schaeffer SW, Russo S, Xu M, Smith TF, Gelbart WM . Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes
Genetics, 2008,179(3):1657-1680.
DOI:10.1534/genetics.107.086108URLPMID:18622036 [本文引用: 1]
The availability of 12 complete genomes of various species of genus Drosophila provides a unique opportunity to analyze genome-scale chromosomal rearrangements among a group of closely related species. This article reports on the comparison of gene order between these 12 species and on the fixed rearrangement events that disrupt gene order. Three major themes are addressed: the conservation of syntenic blocks across species, the disruption of syntenic blocks (via chromosomal inversion events) and its relationship to the phylogenetic distribution of these species, and the rate of rearrangement events over evolutionary time. Comparison of syntenic blocks across this large genomic data set confirms that genetic elements are largely (95%) localized to the same Muller element across genus Drosophila species and paracentric inversions serve as the dominant mechanism for shuffling the order of genes along a chromosome. Gene-order scrambling between species is in accordance with the estimated evolutionary distances between them and we find it to approximate a linear process over time (linear to exponential with alternate divergence time estimates). We find the distribution of synteny segment sizes to be biased by a large number of small segments with comparatively fewer large segments. Our results provide estimated chromosomal evolution rates across this set of species on the basis of whole-genome synteny analysis, which are found to be higher than those previously reported. Identification of conserved syntenic blocks across these genomes suggests a large number of conserved blocks with varying levels of embryonic expression correlation in Drosophila melanogaster. On the other hand, an analysis of the disruption of syntenic blocks between species allowed the identification of fixed inversion breakpoints and estimates of breakpoint reuse and lineage-specific breakpoint event segregation.

[87] Corbett-Detig RB, Hartl DL . Population genomics of inversion polymorphisms in Drosophila melanogaster
PLoS Genet, 2012,8(12):e1003056.
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[88] Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Harvard FlyBase curators, Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Nature, 2007,450(7167):219-232.
DOI:10.1038/nature06340URLPMID:17994088 [本文引用: 1]
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.

[89] Ladoukakis ED, Pereira V, Magny EG, Eyre-Walker A, Couso JP . Hundreds of putatively functional small open reading frames in Drosophila
Genome Biol, 2011,12(11):1-17.
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[90] Lewis SH, Salmela H, Obbard DJ . Duplication and diversification of Dipteran argonaute genes, and the evolutionary divergence of Piwi and Aubergine
Genome Biol Evol, 2016,8(3):507-518.
DOI:10.1093/gbe/evw018URLPMID:26868596 [本文引用: 1]
Genetic studies of Drosophila melanogaster have provided a paradigm for RNA interference (RNAi) in arthropods, in which the microRNA and antiviral pathways are each mediated by a single Argonaute (Ago1 and Ago2) and germline suppression of transposable elements is mediated by a trio of Piwi-subfamily Argonaute proteins (Ago3, Aub, and Piwi). Without a suitable evolutionary context, deviations from this can be interpreted as derived or idiosyncratic. Here we analyze the evolution of Argonaute genes across the genomes and transcriptomes of 86 Dipteran species, showing that variation in copy number can occur rapidly, and that there is constant flux in some RNAi mechanisms. The lability of the RNAi pathways is illustrated by the divergence of Aub and Piwi (182-156 Ma), independent origins of multiple Piwi-family genes in Aedes mosquitoes (less than 25Ma), and the recent duplications of Ago2 and Ago3 in the tsetse fly Glossina morsitans. In each case the tissue specificity of these genes has altered, suggesting functional divergence or innovation, and consistent with the action of dynamic selection pressures across the Argonaute gene family. We find there are large differences in evolutionary rates and gene turnover between pathways, and that paralogs of Ago2, Ago3, and Piwi/Aub show contrasting rates of evolution after duplication. This suggests that Argonautes undergo frequent evolutionary expansions that facilitate functional divergence.

[91] Mohammed J, Flynt AS, Panzarino A, Mondal MH, Decruz M, Siepel A, Lai EC . Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
Genome Res, 2018,28(1):52-65.
DOI:10.1101/gr.226068.117URLPMID:29233922 [本文引用: 1]
To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5' end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3' untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.

[92] Mallet J, Besansky N, Hahn MW . How reticulated are species?
BioEssays, 2016,38(2):140-149.
DOI:10.1002/bies.201500149URLPMID:26709836 [本文引用: 1]
Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.

[93] Severson DW, Behura SK . Mosquito genomics: Progress and challenges
Annu Rev Entomol, 2012,57(1):143-166.
[本文引用: 1]

[94] Oppenheim SJ, Rosenfeld JA, Desalle R . Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors
BMC Genomics, 2017,18(1):205-205.
DOI:10.1186/s12864-017-3590-0URLPMID:28241792 [本文引用: 1]
BACKGROUND: The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. RESULTS: The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. CONCLUSIONS: Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they generate. We believe that efforts to maximize the amount of information obtained from automated annotation can help address the functional annotation deficit that most evolutionary biologists now face, and here demonstrate the value of such an approach.

[95] Singh ND, Larracuente AM, Sackton TB, Clark AG . Comparative genomics on the Drosophila phylogenetic tree
Annu Rev Ecol System, 2009,40:459-480.
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[96] Markow TA . The secret lives of Drosophila flies
eLife, 2015,4:e06793.
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[97] He QY, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J . High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
Nat Genet, 2011,43(5):414-420.
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The binding of some transcription factors has been shown to diverge substantially between closely related species. Here we show that the binding of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at its enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their combinatorial binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. These results suggest that developmental enhancers can be highly evolutionarily constrained, presumably because of their complex combinatorial nature.

[98] Carl S, Russell S. Comparative genomics of transcription factor binding in Drosophila. In: Edited by Raman C, Goldsmith MR, Agunbiade TA. Short Views on Insect Genomics and Proteomics
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[99] Gloss AD, Vass?o DG, Hailey AL, Dittrich ACN, Schramm K, Reichelt M, Rast TJ, Weichsel A, Cravens MG, Gershenzon J, Montfort WM, Whiteman NK . Evolution in an ancient detoxification pathway is coupled with a transition to herbivory in the Drosophilidae
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[100] Goldman-Huertas B, Mitchell RF, Lapoint RT, Faucher CP, Hildebrand JG, Whiteman NK . Evolution of herbivory in Drosophilidae linked to loss of behaviors, antennal responses, odorant receptors, and ancestral diet
Proc Natl Acad Sci USA, 2015,112(10):3026-3031.
DOI:10.1073/pnas.1424656112URLPMID:25624509 [本文引用: 1]
Herbivory is a key innovation in insects, yet has only evolved in one-third of living orders. The evolution of herbivory likely involves major behavioral changes mediated by remodeling of canonical chemosensory modules. Herbivorous flies in the genus Scaptomyza (Drosophilidae) are compelling species in which to study the genomic architecture linked to the transition to herbivory because they recently evolved from microbe-feeding ancestors and are closely related to Drosophila melanogaster. We found that Scaptomyza flava, a leaf-mining specialist on plants in the family (Brassicaceae), was not attracted to yeast volatiles in a four-field olfactometer assay, whereas D. melanogaster was strongly attracted to these volatiles. Yeast-associated volatiles, especially short-chain aliphatic esters, elicited strong antennal responses in D. melanogaster, but weak antennal responses in electroantennographic recordings from S. flava. We sequenced the genome of S. flava and characterized this species' odorant receptor repertoire. Orthologs of odorant receptors, which detect yeast volatiles in D. melanogaster and mediate critical host-choice behavior, were deleted or pseudogenized in the genome of S. flava. These genes were lost step-wise during the evolution of Scaptomyza. Additionally, Scaptomyza has experienced gene duplication and likely positive selection in paralogs of Or67b in D. melanogaster. Olfactory sensory neurons expressing Or67b are sensitive to green-leaf volatiles. Major trophic shifts in insects are associated with chemoreceptor gene loss as recently evolved ecologies shape sensory repertoires.

[101] Hickner PV, Rivaldi CL, Johnson CM, Siddappaji M, Raster GJ, Syed Z . The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii
BMC Genomics, 2016,17(1):648-648.
[本文引用: 1]

[102] Fontaine MC . Genetic diversity of the African malaria vector Anopheles gambiae
Nature, 2017,552(7683):96-100.
DOI:10.1038/nature24995URLPMID:29186111 [本文引用: 1]
The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease. To gain a deeper understanding of how mosquito populations are evolving, here we sequenced the genomes of 765 specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across Africa, and identified over 50 million single nucleotide polymorphisms within the accessible genome. These data revealed complex population structure and patterns of gene flow, with evidence of ancient expansions, recent bottlenecks, and local variation in effective population size. Strong signals of recent selection were observed in insecticide-resistance genes, with several sweeps spreading over large geographical distances and between species. The design of new tools for mosquito control using gene-drive systems will need to take account of high levels of genetic diversity in natural mosquito populations.

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DOI:10.1016/j.cois.2018.01.007URLPMID:29602357 [本文引用: 1]
Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.

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[108] Zhou H, Shen J . Research on functional genomics of agriculture insects: Review and prospect
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