双翅目昆虫基因组研究进展

doi:10.16288/j.yczz.20-130

遗传 ›› 2020, Vol. 42 ›› Issue (11): 1093-1109.doi: 10.16288/j.yczz.20-130

双翅目昆虫基因组研究进展

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

收稿日期:2020-05-06 修回日期:2020-09-06 出版日期:2020-11-20 发布日期:2020-10-20
通讯作者: 韩宝瑜 E-mail:pengwei@cjlu.edu.cn;hanby15@163.com
作者简介:彭威,博士,讲师,研究方向：昆虫生物化学与分子生物学。E-mail:
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)

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

Received:2020-05-06 Revised:2020-09-06 Online:2020-11-20 Published:2020-10-20
Contact: Han Baoyu E-mail:pengwei@cjlu.edu.cn;hanby15@163.com
Supported by:
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)

摘要/Abstract

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.

Key words: Diptera, genome characteristics, functional genes, comparative genomics, phyletic evolution

彭威, 冯蒙洁, 陈皓, 韩宝瑜. 双翅目昆虫基因组研究进展[J]. 遗传, 2020, 42(11): 1093-1109.

Wei Peng, Mengjie Feng, Hao Chen, Baoyu Han. Progress on genome sequencing of Dipteran insects[J]. Hereditas(Beijing), 2020, 42(11): 1093-1109.

图/表 1

表1

双翅目昆虫基因组信息汇总"

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]
食虫虻科 (Asilidae)	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]
萤蚊科 (Chaoboridae)	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]
突眼蝇科 (Diopsidae)	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]
水蝇科 (Ephydridae)	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]
蚤蝇科 (Phoridae)	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]
麻蝇科 (Sarcophagidae)	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]

表1

参考文献 109

[1]	Wiegmann BM, Yeates DK,. Phylogeny of Diptera. 2017, Chapter 11. In Manual of Afrotropical Diptera. Volume 1. Introductory Chapters and Keys to Diptera Families Suricata. Edited by Kirk-Spriggs AH, Sinclair BJ. SANBI Graphics & Editing.
[2]	Wiegmann BM, Trautwein M, Winkler IS, Barr NB, Kim J, Lambkin CL, Bertone MA, Cassel BK, Bayless KM, Heimberg AM, Wheeler BM, Peterson KJ, Pape T, Sinclair BJ, Skevington JH, Blagoderov V, Caravas J, Kutty SN, Schmidt-Ott U, Kampmeier GE, Thompson FC, Grimaldi DA, Beckenbach AT, Courtney GW, Friedrich M, Meier R, Yeatesd DK . Episodic radiations in the fly tree of life. Proc Natl Acad Sci USA, 2011,108(14):5690-5695.
[3]	Bertone MA, Courtney GW, Wiegmann BM . Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes. Syst Entomol, 2008,33(4):668-687.
[4]	Labandeira CC. Fossil history and evolutionary ecology of Diptera and their associations with plants. The evolutionary biology of flies. Columbia University Press, 2005, 217-273.
[5]	Ssymank A, Kearns CA, Pape T, Thompson FC . Pollinating flies (Diptera): A major contribution to plant diversity and agricultural production. Biodiversity, 2008,9(1-2):86-89.
[6]	Wiens JJ, Lapoint RT, Whiteman NK . Herbivory increases diversification across insect clades. Nat Commun, 2015,6(1):8370-8370.
[7]	Vicoso B, Bachtrog D . Numerous transitions of sex chromosomes in Diptera. PLoS Biol, 2015,13(4):e1002078. pmid: 25879221
[8]	Dikow RB, Frandsen PB, Turcatel M, Dikow T . Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti(Insecta: Diptera: Asilidae) and 16 representative transcriptomes. PeerJ, 2017,5:e2951.
[9]	Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua SJ, Smith MA, Zhang PL, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang YM, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MAF, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res, 2005,15(1):1-18.
[10]	Bellen HJ, Levis RW, He YC, Carlson JW, Evans-Holm M, Bae E, Kim J, Metaxakis A, Savakis C, Schulze KL, Hoskins RA, Spradling AC . The Drosophila gene disruption project: progress using transposons with distinctive site specificities. Genetics, 2011,188(3):731-743. doi: 10.1534/genetics.111.126995 pmid: 21515576
[11]	Gratz SJ, Ukken FP, Rubinstein CD, Thiede G, Donohue LK, Cummings AM, O’connor-Giles KM . Highly specific and efficient CRISPR/Cas9-catalyzed homology- directed repair in Drosophila. Genetics, 2014,196(4):961-971. pmid: 24478335
[12]	Xue ZY, Wu MH, Wen KJ, Ren MD, Long L, Zhang XD, Gao GJ . CRISPR/Cas9 mediates efficient conditional mutagenesis in Drosophila. G3 (Bethesda), 2014,4(11):2167-2173.
[13]	Jory A, Estella C, Giorgianni MW, Slattery M, Laverty TR, Rubin GM, Mann RS . A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Rep, 2012,2(4):1014-1024. pmid: 23063361
[14]	Geib SM, Calla B, Hall B, Hou SB, Manoukis NC . Characterizing the developmental transcriptome of the oriental fruit fly,Bactrocera dorsalis( Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics, 2014,15(1):942-942.
[15]	Grönke S, Clarke DF, Broughton S, Andrews TD, Partridge L . Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet, 2010,6(2):e1000857.
[16]	Neely GG, Hess A, Costigan M, Keene AC, Goulas S, Langeslag M, Griffin RS, Belfer I, Dai F, Smith SB, Diatchenko L, Gupta V, Xia CP, Amann S, Kreitz S, Heindl-Erdmann C, Wolz S, Ly CV, Arora S, Sarangi R, Dan D, Novatchkova M, Rosenzweig M, Gibson DG, Truong D, Schramek D, Zoranovic T, Cronin SJF, Angjeli B, Brune K, Dietzl G, Maixner W, Meixner A, Thomas W, Pospisilik JA, Alenius M, Kress M, Subramaniam S, Garrity PA, Bellen HJ, Woolf CJ, Penninger JM . A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Cell, 2010,143(4):628-638. pmid: 21074052
[17]	Mahajan S, Bachtrog D . Convergent evolution of Y chromosome gene content in flies. Nat Commun, 2017,8(1):785-785. pmid: 28978907
[18]	Dermauw W, Van Leeuwen T . The ABC gene family in arthropods: Comparative genomics and role in insecticide transport and resistance. Insect Biochem Mol Biol, 2014,45:89-110. doi: 10.1016/j.ibmb.2013.11.001 pmid: 24291285
[19]	Scott JG, Warren WC, Beukeboom LW, Bopp D, Clark AG, Giers SD, Hediger M, Jones AK, Kasai S, Leichter CA, Li M, Meisel RP, Minx P, Murphy TD, Nelson DR, Reid WR, Rinkevich FD, Robertson HM, Sackton TB, Sattelle DB, Thibaud-Nissen F, Tomlinson C, van de Zande L, Walden KK, Wilson RK, Liu NN. Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment. Genome Biol, 2014,15(10):466-466. doi: 10.1186/s13059-014-0466-3 pmid: 25315136
[20]	Groen SC, Whiteman NK . Using Drosophila to study the evolution of herbivory and diet specialization. Curr Opin Insect Sci, 2016,14:66-72.
[21]	Bergland AO, Tobler R, González J, Schmidt PS, Petrov D . Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Mol Ecol, 2016,25(5):1157-1174. doi: 10.1111/mec.13455 pmid: 26547394
[22]	Ramasamy S, Ometto L, Crava CM, Revadi S, Kaur R, Horner DS, Pisani D, Dekker T, Anfora G, Rota-Stabelli O . The evolution of olfactory gene families in Drosophila and the genomic basis of chemical-ecological adaptation in Drosophila suzukii. Genome Biol Evol, 2016,8(8):2297-2311.
[23]	Cicconardi F, Di Marino D, Olimpieri PP, Arthofer W, Schlick-Steiner BC, Steiner FM . Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics’ and structural biology’s lenses. Sci Rep, 2017,7(1):43770.
[24]	Misof B, Liu SL, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspöck U, Aspöck H, Bartel D, Blanke A, Berger S, Böhm A, Buckley TR, Calcott B, Chen JQ, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu SC, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li YY, Li ZY, Li JG, Lu HR, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng GL, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou YX, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schütte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song WH, Su X, Szucsich NU, Tan MH, Tan XM, Tang M, Tang JB, Timelthaler G, Tomizuka S, Trautwein M, Tong XL, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TKF, Wu Q, Wu GX, Xie YL, Yang SZ, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang WW, Zhang YH, Zhao J, Zhou CR, Zhou LL, Ziesmann T, Zou SJ, Li YR, Xu X, Zhang Y, Yang HM, Wang J, Wang J, Kjer KK, Zhou X. Phylogenomics resolves the timing and pattern of insect evolution. Science, 2014,346(6210):763-767. pmid: 25378627
[25]	Kutty SN, Wong WH, Meusemann K, Meier R, Cranston P . A phylogenomic analysis of Culicomorpha(Diptera) resolves the relationships among the eight constituent families. Syst Entomol, 2018,43(3):434-446.
[26]	Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JMC, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai ZW, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chatuverdi K, Christophides FK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu ZP, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke ZX, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao HG, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun JT, Thomasova D, Ton LQ, Topalis P, Tu ZJ, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang XL, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang HY, Zhao Q, Zhao SY, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL. The genome sequence of the malaria mosquito Anopheles gambiae. Science, 2002,298(5591):129-149.
[27]	Arensburger P, Megy K, Waterhouse RM, Abrudan JL, Amedeo P, Antelo BG, Bartholomay LC, Bidwell SL, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao CH, Mayhew G, Michel K, Mori A, Liu NN, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi YM, Ranson H, Ribeiro JMC, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JMC, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MAT, Raikhel AS, Atkinson PW . Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science, 2010,330(6000):86-88. pmid: 20929810
[28]	Logue K, Small ST, Chan ER, Reimer LJ, Siba P, Zimmerman PA, Serre D . Whole-genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea. Mol Ecol, 2015,24(6):1263-1274. pmid: 25677924
[29]	Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL . De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017,356(6333):92-95. pmid: 28336562
[30]	Artemov GN, Peery AN, Jiang XF, Tu ZJ, Stegniy VN, Sharakhova MV, Sharakhov IV . The physical genome mapping of Anopheles albimanus corrected scaffold misassemblies and identified interarm rearrangements in genus Anopheles. G3 (Bethesda), 2017,7(1):155-164.
[31]	Neafsey DE, Waterhouse RM, Abai MR, Aganezov S, Alekseyev MA, Allen JE, Amon J, Arca B, Arensburger P, Artemov GN, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang XF, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou XF, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu ZJ, Zwiebel LJ, Besansky NJ. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes. Science, 2015,347(6217):1258522-1258522.
[32]	Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides P, Scherer S, Li PW, Hoskins RA, Galle R, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris ML, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Woodage T, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science, 2000,287(5461):2185-2195.
[33]	Zhou Q, Bachtrog D . Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science, 2012,337(6092):341-345.
[34]	Chen ZX, Sturgill D, Qu JX, Jiang HY, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, Fitzgerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee AL, Li MM, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou XY, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S . Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res, 2014,24(7):1209-1223. doi: 10.1101/gr.159384.113 pmid: 24985915
[35]	Sanchez-Flores A, Peñaloza F, Carpinteyro-Ponce J, Nazario-Yepiz NO, Abreu-Goodger C, Machado CA, Markow TA . Genome evolution in three species of cactophilic Drosophila. G3 (Bethesda), 2016,6(10):3097-3105.
[36]	Khanna R, Mohanty S . Whole genome sequence resource of Indian Zaprionus indianus. Mol Ecol Res, 2017,17(3):557-564.
[37]	Mohanty S, Khanna R . Genome-wide comparative analysis of four Indian Drosophila species. Mol Genet Genom, 2017,292(6):1197-1208.
[38]	Fuller ZL, Haynes GD, Richards S, Schaeffer SW . Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura. Mol Ecol, 2017,26(23):6539-6562. pmid: 29055159
[39]	Clark AG, Eisen MB, Smith D, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart WM, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li RQ, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long MY, Low L, Lozovsky E, Lu J, Luo MZ, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang PL, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu XH, Liu JL, Liu ST, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong DN, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I, . Evolution of genes and genomes on the Drosophila phylogeny. Nature, 2007,450(7167):203-218.
[40]	Lack JB, Lange JD, Tang AD, Corbett-Detig RB, Pool JE . A thousand fly genomes: an expanded Drosophila genome nexus. Mol Biol Evol, 2016,33(12):3308-3313. pmid: 27687565
[41]	Stanley CE, Kulathinal RJ,. flyDIVaS: A comparative genomics resource for Drosophila divergence and selection. G3 (Bethesda), 2016,6(8):2355-2363.
[42]	Mackay TFC, Huang W . Charting the genotype- phenotype map: lessons from the Drosophila melanogaster genetic reference panel. Wiley Interdiscip Rev Dev Biol, 2018,7(1), e289.
[43]	Anstead CA, Korhonen PK, Young ND, Hall RS, Jex AR, Murali SC, Hughes DST, Lee SF, Perry T, Stroehlein AJ, Ansell BRE, Breugelmans B, Hofmann AS, Qu JX, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ioannidis P, Waterhouse RM, Zdobnov EM, James PJ, Bagnall NH, Kotze AC, Gibbs RA, Richards S, Batterham P, Gassera RB . Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions. Nat Commun, 2015,6(1):7344-7344.
[44]	Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castanera P, Cavanaugh JP, Chao H, Childers CP, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, González-Guzmán M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernández-Crespo P, Hughes DST, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu JX, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Ureña E, Vlachos IS, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM . The whole genome sequence of the Mediterranean fruit fly,Ceratitis capitata(Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol, 2016,17(1):192. pmid: 27659211
[45]	Zhao CY, Escalante LN, Chen H, Benatti TR, Qu JX, Chellapilla S, Waterhouse RM, Wheeler D, Andersson MN, Bao RY, Batterton M, Behura SK, Blankenburg KP, Caragea D, Carolan JC, Coyle M, El-Bouhssini M, Francisco L, Friedrich M, Gill N, Grace T, Grimmelikhuijzen CJP, Han Y, Hauser F, Herndon N, Holder M, Ioannidis P, Jackson L, Javaid M, Jhangiani SN, Johnson AJ, Kalra D, Korchina V, Kovar CL, Lara F, Lee SL, Liu XM, Löfstedt C, Mata R, Mathew T, Muzny DM, Nagar S, Nazareth LV, Okwuonu G, Ongeri F, Perales L, Peterson BF, Pu LL, Robertson HM, Schemerhorn BJ, Scherer SE, Shreve JT, Simmons D, Subramanyam S, Thornton RL, Xue K, Weissenberger GM, Williams CE, Worley KC, Zhu DH, Zhu YM, Harris MO, Shukle RH, Werren JH, Zdobnov EM, Chen MS, Brown SJ, Stuart JJ, Richards S . A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor. Curr Biol, 2015,25(5):613-620. pmid: 25660540
[46]	Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L . The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics, 2014,15(1):819-819.
[47]	Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen L, Betancourt AJ, Hummel T, Vogel H, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K, . The genomic basis of circadian and circalunar timing adaptations in a midge. Nature, 2016,540(7631):69-73.
[48]	Andere AA, Platt RN, Ray DA, Picard CJ . Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research. BMC Genomics, 2016,17(1):842. doi: 10.1186/s12864-016-3187-z pmid: 27793085
[49]	Watanabe J, Hattori M, Berriman M, Lehane MJ, Hall N, Solano P, Aksoy S, Hide W, Toure YT, Attardo GM . Genome sequence of the tsetse fly (glossina morsitans): vector of African trypanosomiasis. Science, 2014,344(6182):380-386.
[50]	Rasmussen DA, Noor MA . What can you do with 01×genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris(Phoridae). BMC Genomics, 2009,10:382. pmid: 19689807
[51]	Kelley JL, Peyton JT, Fiston-Lavier AS, Teets NM, Yee MC, Johnston JS, Bustamante CD, Lee RE, Denlinger DL . Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nat Commun, 2014,5(1):4611-4611.
[52]	Nene V, Wortman JR, Lawson D, Haas BJ, Kodira CD, Tu ZJ, Loftus BJ, Xi ZY, Megy K, Grabherr M, Ren QH, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu JS, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao CH, Mauceli E, Menck CFM, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JMC, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng QD, Zhao Q, Zhao TM, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW,. Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 2007,316(5832):1718-1723.
[53]	Huang W, Massouras A, Inoue Y, Peiffer JA, Ramia M, Tarone AM, Turlapati L, Zichner T, Zhu DH, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu LL, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang YQ, Zhu YM, Anholt RR, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TFC . Natural variation in genome architecture among 205 Drosophila melanogaster genetic reference panel lines. Genome Res, 2014,24(7):1193-1208. doi: 10.1101/gr.171546.113 pmid: 24714809
[54]	Huang W, Richards S, Carbone MA, Zhu DH, Anholt RRH, Ayroles JF, Duncan LH, Jordan KW, Lawrence F, Magwire MM, Warner CB, Blankenburg K, Han Y, Javaid M, Jayaseelan J, Jhangiani SN, Muzny D, Ongeri F, Perales L, Wu YQ, Zhang YQ, Zou XY, Stone EA, Gibbs RA, Mackay TFC . Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci USA, 2012,109(39):15553-15559. doi: 10.1073/pnas.1213423109 pmid: 22949659
[55]	Mackay TFC, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu DH, Casillas S, Han Y, Magwire MM, Cridland JM, Richardson MF, Anholt RR, Barrón M, Bess C, Blankenburg KP, Carbone MA, Castellano D, Chaboub L, Duncan L, Harris Z, Javaid M, Jayaseelan JC, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P, Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DM, Nazareth L, Newsham I, Perales L, Pu LL, Qu C, Ràmia M, Reid JG, Rollmann SM, Rozas J, Saada N, Turlapati L, Worley KC, Wu YQ, Yamamoto A, Zhu YM, Bergman CM, Thornton KR, Mittelman D, Gibbs RA . The Drosophila melanogaster genetic reference panel. Nature, 2012,482(7384):173-178.
[56]	Obbard DJ, Maclennan J, Kim KW, Rambaut A, O’grady PM, Jiggins FM . Estimating divergence dates and substitution rates in the Drosophila phylogeny. Mol Biol Evol, 2012,29(11):3459-3473.
[57]	Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani EG . Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science, 2015,347(6217):1258524-1258524.
[58]	Savard J, Tautz D, Lercher MJ . Genome-wide acceleration of protein evolution in flies (Diptera). BMC Evol Biol, 2006,6(1):7-7.
[59]	Zdobnov EM, Bork P . Quantification of insect genome divergence. Trends Genet, 2007,23(1):16-20. doi: 10.1016/j.tig.2006.10.004 pmid: 17097187
[60]	Zdobnov EM, Von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai ZW, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P . Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science, 2002,298(5591):149-159.
[61]	Craddock EM, Gall JG, Jonas M . Hawaiian Drosophila genomes: size variation and evolutionary expansions. Genetica, 2016,144(1):107-124. pmid: 26790663
[62]	Elliott TA, Gregory TR . What's in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philos Trans R Soc Lond B Biol Sci, 2015,370(1678):20140331. pmid: 26323762
[63]	Bargues N, Lerat E . Evolutionary history of LTR-retrotransposons among 20 Drosophila species. Mob DNA, 2017,8(1):7-7.
[64]	Waterhouse RM . A maturing understanding of the composition of the insect gene repertoire. Curr Opin Insect Sci, 2015,7:15-23.
[65]	Feyereisen R. Insect CYP genes and P450 enzymes. In: Gilbert LI, editor. Insect Molecular Biology and Biochemistry, Oxford: Elsevier; 2012. p. 237-316.
[66]	Arouri R, Le Goff G, Hemden H, Navarro-Llopis V, M’Saad M, Castanera P, Feyereisen R, Hernández- Crespo P, Ortego F,. Resistance to lambda-cyhalothrin in Spanish field populations of Ceratitis capitata and metabolic resistance mediated by P450 in a resistant strain. Pest Manag Sci, 2015,71(9):1281-1291.
[67]	Lemaitre B, Hoffmann J . The host defense of Drosophila melanogaster. Annu Rev Immunol, 2007,25(1):697-743.
[68]	Boutros M, Agaisse H, Perrimon N . Sequential activation of signaling pathways during innate immune responses in Drosophila. Dev Cell, 2002,3(5):711-722.
[69]	Kang DW, Liu G, Lundström A, Gelius E, Steiner H . A peptidoglycan recognition protein in innate immunity conserved from insects to humans. Proc Natl Acad Sci USA, 95(17):10078-10082. pmid: 9707603
[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. J Biol Chem, 275(42):32721-32727. doi: 10.1074/jbc.M003934200 pmid: 10827089
[71]	Lee WJ, Lee JD, Kravchenko VV, Ulevitch RJ, Brey PT . Purification and molecular cloning of an inducible gram-negative bacteria-binding protein from the silkworm, Bombyx mori. Proc Natl Acad Sci USA, 1996,93(15):7888-7893.
[72]	Sackton TB, Lazzaro BP, Schlenke TA, Evans JD, Hultmark D, Clark AG . Dynamic evolution of the innate immune system in Drosophila. Nat Genet, 2007,39(12):1461-1468.
[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. BMC Genomics, 2008,9(1):243. doi: 10.1186/1471-2164-9-243
[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. BMC Dev Biol, 10(1):12. doi: 10.1186/1471-213X-10-12
[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. doi: 10.1038/nature06323 pmid: 17994089
[76]	Gnad F, Parsch J . Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression. Bioinformatics, 2006,22(20):2577-2579.
[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.aaa2850 pmid: 25999371
[78]	Krzywinska E, Dennison NJ, Lycett G, Krzywinski J . A maleness gene in the malaria mosquito Anopheles gambiae. Science, 2016,353(6294):67-69. doi: 10.1126/science.aaf5605 pmid: 27365445
[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. pmid: 28495751
[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.aax1318 pmid: 31467189
[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.103713.109 pmid: 20601587
[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. pmid: 25244985
[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.076588.108 pmid: 18550802
[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.1248286 pmid: 24457212
[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/nrg3627 pmid: 24296533
[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.107.086108 pmid: 18622036
[87]	Corbett-Detig RB, Hartl DL . Population genomics of inversion polymorphisms in Drosophila melanogaster. PLoS Genet, 2012,8(12):e1003056. pmid: 23284285
[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/nature06340 pmid: 17994088
[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.
[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/evw018 pmid: 26868596
[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.226068.117 pmid: 29233922
[92]	Mallet J, Besansky N, Hahn MW . How reticulated are species? BioEssays, 2016,38(2):140-149. doi: 10.1002/bies.201500149 pmid: 26709836
[93]	Severson DW, Behura SK . Mosquito genomics: Progress and challenges. Annu Rev Entomol, 2012,57(1):143-166.
[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/s12864-017-3590-0 pmid: 28241792
[95]	Singh ND, Larracuente AM, Sackton TB, Clark AG . Comparative genomics on the Drosophila phylogenetic tree. Annu Rev Ecol System, 2009,40:459-480.
[96]	Markow TA . The secret lives of Drosophila flies. eLife, 2015,4:e06793.
[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. doi: 10.1038/ng.808 pmid: 21478888
[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. Springer International Publishing, 2015.
[99]	Gloss AD, Vassão 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. Mol Biol Evol, 2014,31(9):2441-2456.
[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.1424656112 pmid: 25624509
[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.
[102]	Fontaine MC . Genetic diversity of the African malaria vector Anopheles gambiae. Nature, 2017,552(7683):96-100. doi: 10.1038/nature24995 pmid: 29186111
[103]	Wiegmann BM, Richards S . Genomes of Diptera. Curr Opin Insect Sci, 2018,25:116-124. doi: 10.1016/j.cois.2018.01.007 pmid: 29602357
[104]	Simon CR, Siviero F, Monesi N . Beyond DNA puffs: What can we learn from studying sciarids? Genesis, 2016,54(7):361-378. pmid: 27178805
[105]	Hou L, Zhan S, Zhou X, Li F, Wand XH . Advances in research on insect genomics in China. Chin Bull Entomol, 2017,54(5):693-704.
	侯丽, 詹帅, 周欣, 李飞, 王宪辉 . 中国昆虫基因组学的研究进展. 应用昆虫学报, 2017,54(5):693-704.
[106]	Zhang CX . Current research status and prospects of genomes of insects important to agriculture in China. Sci Agric Sin, 2015,48(17):3454-3462.
	张传溪 . 中国农业昆虫基因组学研究概况与展望. 中国农业科学, 2015,48(17):3454-3462.
[107]	Ye GY, Fang Q . Entomological research in the genomic age. Chin Bull Entomol, 2011,48(6):1531-1538.
	叶恭银, 方琦 . 基因组时代的昆虫学研究. 应用昆虫学报, 2011,48(6):1531-1538.
[108]	Zhou H, Shen J . Research on functional genomics of agriculture insects: Review and prospect. J Enviro Entomol, 2017,39(2):239-248.
	周行, 沈杰 . 农业昆虫的功能基因组学研究: 回顾与展望. 环境昆虫学报, 2017,39(2):239-248.
[109]	Yin CL, Li MZ, He K, Ding SM, Guo DH, Xi Y, Li F . The progress of insecg genomic research and the gene database. J Enviro Entomol, 2017,39(1):1-18.
	尹传林, 李美珍, 贺康, 丁思敏, 郭殿豪, 席羽, 李飞 . 昆虫基因组及数据库研究进展. 环境昆虫学报, 2017,39(1):1-18.

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