彭威，馮蒙潔，陳皓，韓寶瑜

綜 述

雙翅目昆蟲基因組研究進展

彭威，馮蒙潔，陳皓，韓寶瑜

中國計量大學，浙江省生物計量及檢驗檢疫技術(shù)重點實驗室，杭州 310018

雙翅目(Diptera)是完全變態(tài)昆蟲中種類最多樣化的昆蟲，也是第一個基因組已完整測序的昆蟲。目前共有110種雙翅目昆蟲具有公開的基因組，其中黑腹果蠅()和岡比亞按蚊()包含數(shù)百個種群基因組。比較基因組學闡明了雙翅目昆蟲的多種生物學問題，為基因組結(jié)構(gòu)變異、遺傳機制以及基因、物種、種群的進化速率和進化模式的研究提供了新思路。盡管雙翅目昆蟲基因組資源豐富，但仍有許多物種缺乏基因組信息。雙翅目昆蟲基因組研究對于揭示吸血、寄生、授粉和噬菌性等重要行為的多重起源具有重要價值。本文主要介紹了雙翅目昆蟲基因組的分布和不同物種基因組的特性，以及雙翅目昆蟲基因組中功能基因如細胞色素P450、免疫、性別決定和分化相關(guān)基因的研究進展，對雙翅目昆蟲比較基因組學中的重大發(fā)現(xiàn)進行了總結(jié)，以期在快速發(fā)展的基因組組學時代為其他物種進行基因組測序提供指導和借鑒，為開發(fā)基于基因組的害蟲防治和治理提供理論基礎。

雙翅目昆蟲；基因組特性；功能基因；比較基因組學；系統(tǒng)進化

昆蟲是動物界種類最豐富的古老類群。目前地球上已知的昆蟲有100萬種左右，估計全世界昆蟲總數(shù)在1000萬種以上。其中，雙翅目(Diptera)昆蟲分布廣、數(shù)量大、種類多樣化，大約包含180個屬，總計158,000個種，分為5個主要的下目，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)[1~3]。短角下目包括約20個總科，總計80,000個物種。其中包括起源于1.8億年前的短角亞目(Lower Brachycera)和起源于0.65億年前的環(huán)裂亞目(Cyclorrhapha)。環(huán)裂亞目超過78個科，習性多樣，包括植食性、寄生性、食真菌、哺乳動物寄生性、蛆病、吸血以及幼蟲取食腐爛有機質(zhì)的腐食性。另外，重要的傳粉昆蟲如食蚜蠅科(Syrphidae)和蜂虻科(Bombyliidae)也主要分布在環(huán)裂亞目。在傳粉昆蟲和開花植物互作中，適應和提高傳粉的能力是雙翅目昆蟲形態(tài)多樣性、物種多樣性和生態(tài)多樣性的重要驅(qū)動力[4~6]。雙翅目既包括造成巨大生產(chǎn)損失的農(nóng)業(yè)害蟲如地中海實蠅()、麥癭蚊()和絲光綠蠅()，又包括危害健康的衛(wèi)生害蟲如家蠅()、埃及伊蚊()和岡比亞按蚊()。其中蚊蟲叮咬傳播的疾病每年可導致200萬人死亡。雙翅目昆蟲中也有為農(nóng)業(yè)生態(tài)系統(tǒng)中的開花植物提供授粉的傳粉昆蟲如食蚜蠅科和蜂虻科。雙翅目昆蟲生活史、行為習性、取食習性和形態(tài)適應性具有多樣性[1]。

模式物種黑腹果蠅()，媒介昆蟲如埃及伊蚊、岡比亞按蚊和采采蠅()，農(nóng)業(yè)害蟲如地中海實蠅、麥癭蚊和絲光綠蠅是雙翅目昆蟲中早期完成基因組完整測序的物種。同時，非模式物種基因組測序物種的數(shù)量也在增加[7,8]。目前雙翅目昆蟲中有多達110個物種已完成且可公開獲取完整的基因組序列信息(http:// i5k.github.io/arthropod_genomes_at_ncbi)。雙翅目昆蟲基因組測序數(shù)量的穩(wěn)步增長、以及系統(tǒng)發(fā)育基因組學和比較基因組學的發(fā)展為研究種間和種內(nèi)水平的昆蟲遺傳機制和進化過程提供了新的視角。雙翅目昆蟲基因組測序樣本覆蓋率的增加為評估果蠅屬和蚊子外物種進化提供了極為重要的參考。雙翅目昆蟲種間和種內(nèi)的系統(tǒng)發(fā)育基因組學和比較基因組學已經(jīng)在基因調(diào)控和修復[9~12]、發(fā)育[13,14]、神經(jīng)生物學[15,16]、性別決定[17]、昆蟲抗藥性[18,19]、營養(yǎng)?；痆20]和生態(tài)適應[21~23]等方面產(chǎn)生了重大的研究成果。毫無疑問，通過下一代基因測序技術(shù)和更加完善的基因組數(shù)據(jù)庫，雙翅目昆蟲基因組研究將推動昆蟲基因組學的發(fā)展，從系統(tǒng)生物學的角度來解決昆蟲學研究中的問題，為農(nóng)業(yè)害蟲和病媒昆蟲綠色防控提供新策略。本文綜述了雙翅目昆蟲基因組在不同物種中的分布和研究現(xiàn)狀，介紹了雙翅目昆蟲基因組的特性和雙翅目昆蟲基因組中功能基因如細胞色素P450、免疫、性別決定和分化相關(guān)基因研究進展，總結(jié)了雙翅目昆蟲比較基因組學中的重大發(fā)現(xiàn)，以期為了解雙翅目昆蟲多樣性、生物學特性以及基于基因組的害蟲防治和治理提供參考。

1 雙翅目基因組研究現(xiàn)狀

分子進化、系統(tǒng)發(fā)育和化石等證據(jù)將雙翅目昆蟲的起源定于2.6億年前的二疊紀晚期，大約與其他主要的全變態(tài)昆蟲同時開始出現(xiàn)[2,24]。由于雙翅目物種間巨大的形態(tài)差異、遺傳多樣性和快速進化的歷史進程，對充分闡明雙翅目昆蟲生命進化構(gòu)成了挑戰(zhàn)。但是系統(tǒng)進化基因組學研究有助于促進我們對雙翅目生命進化的理解[1,25]。目前，雙翅目亞目已完成110個物種基因組測序，主要分布在蚊科和果蠅科(表1)。(1)蚊科：按蚊科共完成27個物種基因組測序，鑒定了岡比亞按蚊吸血生理適應性和免疫相關(guān)基因表達，為了解吸血性媒介昆蟲的生理適應機制及瘧疾的發(fā)病機理提供了理論依據(jù)[26]；發(fā)現(xiàn)致倦庫蚊()嗅覺和味覺受體、唾液腺基因和殺蟲劑解毒作用相關(guān)基因家族數(shù)目增加[27]；分析了基因漂流和種群歷史演變[28]；利用Hi-C技術(shù)更新了埃及伊蚊基因組染色體讀長[29]；利用長讀長測序方法對白紋伊蚊()基因組重測序，發(fā)現(xiàn)其N50>3 Mb[30]；對16種按蚊科蚊蟲的基因組比較鑒定出基因倒置和參與病媒競爭基因的快速進化[31]。(2)果蠅科：共完成33個物種基因組測序，主要是Brachycera、Cyclorrhapha、Schizophora、Ephydroidea。其中分析了黑腹果蠅基因組結(jié)構(gòu)，其2/3為常染色質(zhì)，1/3為異染色質(zhì)，異染色質(zhì)主要包括簡單重復序列、中度重復元件和一些單拷貝DNA，鑒定了與DNA復制、染色體行為、轉(zhuǎn)錄和基因調(diào)控等相關(guān)的蛋白家族[32~37]；研究了染色體倒置現(xiàn)象[38]；對12種果蠅、、、、、、、、、、和基因組測序比較分析，發(fā)現(xiàn)其在基因組大小、基因數(shù)量、轉(zhuǎn)座子分布等方面表現(xiàn)出高度保守性，與環(huán)境互作和生殖相關(guān)蛋白編碼基因、非編碼RNA、順式調(diào)節(jié)區(qū)出現(xiàn)變異[39]。對變色伏繞眼果蠅()等10中果蠅性染色體差異的進化模式進行了研究，發(fā)現(xiàn)不同果蠅間性染色體組型存在極大地差異性[7,25]。

隨著高通量測序技術(shù)的發(fā)展，越來越多的非模式雙翅目昆蟲基因組信息得以公布[40~42]。已完成的醫(yī)學或農(nóng)業(yè)重要性物種的基因組測序可為廣大科研工作者探索潛在的害蟲防控機制提供重要參考。雙翅目農(nóng)業(yè)重要性物種基因組測序包括多種作物或果蔬害蟲，如小麥害蟲麥癭蠅和10種實蠅科(Tephri-tidae)害蟲，如地中海實蠅、橄欖果實蠅()。另外，麗蠅科如絲光綠蠅和銅綠蠅()是綿羊蠅蛆病的重要載體，其基因組測序工作具有極其重要的價值[43]。地中海實蠅基因組鑒定超過1800個與入侵和寄主適應相關(guān)基因家族發(fā)生擴張[44]；瓜實蠅()基因組篩選出多個用于害蟲防治研究的候選靶標基因；鑒定了防治銅綠蠅的靶標基因[43]；麥癭蚊基因組鑒定出426個效應家族基因和2個抵御寄主植物抗性基因[45]。雙翅目醫(yī)學重要性物種基因組測序包括多種吸血媒介昆蟲的基因組，如沙蠅3個毛蠓科(Psychodidae)物種、采采蠅6個舌蠅科(Glossinidae)物種和螯蠅1個蠅科(Muscidae)物種；鑒定了搖蚊科唾液腺相關(guān)基因表達和蛋白激酶相關(guān)基因表達[46,47]；伏蠅()基因組可以應用于法醫(yī)鑒定[48]；舌蠅科總共完成6個物種基因組測序，鑒定了泌乳特異蛋白和卵胎生發(fā)育過程[49]；家蠅科中家蠅基因組基因拷貝數(shù)增加，免疫系統(tǒng)識別和效應基因多樣[19]，廄螫蠅()基因組主要用于采采蠅基因組的比較分析；蚤蠅科蛆癥異蚤蠅()基因組起初被用作低覆蓋率基因組分析檢測[50]；由于難以獲取足夠高質(zhì)量長須羅蛉()和巴氏白蛉()DNA，導致毛蠓科基因組測序困難。最近完成超過35個物種基因組測序工作顯著提高了雙翅目昆蟲非模式物種測序覆蓋率和基因組學及性染色體差異的進化模式研究，包括潛蠅科班潛蠅()、食蟲虻科、麗蠅科紅頭麗蠅()和絲光綠蠅、螢蚊科和、搖蚊科、突眼蠅科和、長足蠅科、果蠅科和、實蠅科橄欖果實蠅等[7,8](表1)。

2 雙翅目昆蟲基因組特性

雙翅目昆蟲基因組測序始于環(huán)裂亞目的黑腹果蠅[32]和蚊下目的岡比亞按蚊[26]和埃及伊蚊[52]。黑腹果蠅、岡比亞按蚊和埃及伊蚊基因組的完成不僅催生了基因組數(shù)據(jù)庫、注釋參考文庫以及生物信息學分析的成功建立和發(fā)展，而且極大地推動了國際合作組織對12種果蠅屬和16種按蚊屬雙翅目昆蟲的基因組測序和組裝工作[31,39]。果蠅科種群基因組計劃(population genomics project, DPGP)已收錄超過1121種果蠅科野生種群基因組序列[38]。果蠅基因參考圖譜(genetic reference panel, DPGP)包含205種黑腹果蠅品系全基因組關(guān)聯(lián)分析(genome-wide association study, GWAS)數(shù)據(jù)[53~55]。因此，雙翅目昆蟲基因組的差異性主要來自蚊子和果蠅這兩個分化水平顯著不同的分支。蚊子和果蠅是雙翅目現(xiàn)存世系中最古老的兩個分支，其共同的祖先來自大約2.4億年前[2]。果蠅屬物種分支進化跨度最近為24萬年前，最遠為2200萬年前至5500萬年前之間[56]；按蚊屬物種分支進化跨度最近為54萬年前，最遠為180萬年前至1億年前之間[57]。蚊子與果蠅間、雙翅目其他昆蟲間以及雙翅目與其他目昆蟲間的比較基因組學揭示了雙翅目昆蟲基因組進化速率顯著加快[58]，使得雙翅目昆蟲相對于其他昆蟲而言是名副其實的“長枝”進化物種。而蚊子和果蠅的比較基因組學表明這兩類昆蟲以顯著較大的速率從彼此分化出去，進而進化為雙翅目中兩大類[59,60]。

表1 雙翅目昆蟲基因組信息匯總

續(xù)表1

雙翅目昆蟲基因組大小差異巨大，從毫蚊科的41.57 Mb到白紋伊蚊的2538.37 Mb不等(表1)。即使在同一個科中，基因組的大小也差異很大，按蚊科基因組大小從146.16~ 2538.37 Mb，而果蠅科基因組大小變化相對較小，從117~386 Mb[61]。雙翅目昆蟲基因組大小差異巨大的原因可能是其轉(zhuǎn)座子(TEs)和其他重復非編碼DNA的差異導致[62,63]。TEs不僅介導物種的進化和新基因的形成，而且參與基因組的表觀調(diào)控以及異染色質(zhì)結(jié)構(gòu)的形成。雙翅目昆蟲基因組中存在的大量非編碼DNA是產(chǎn)生遺傳變異的重要來源，影響基因組大小的進化方向。雙翅目昆蟲基因組包含的基因數(shù)量差異很大。黑腹果蠅基因組總共有13,920個基因，致倦庫蚊基因組總共有18,955個基因。雙翅目昆蟲基因組基因數(shù)量最少的是南極蠓()中的13,517個[51]，最多的是家蠅中的23,884個[64]。南極蠓是南極大陸上唯一一種真正意義上的昆蟲，也是南極大陸特有的物種。測序發(fā)現(xiàn)其基因組規(guī)模高度簡化，大約只包含9900萬個堿基對，基因組中重復的基因序列很少，但與代謝功能、生長發(fā)育相關(guān)的基因卻足夠多。南極蠓在漫長的進化過程中，通過剔除非必須基因序列不斷調(diào)整遺傳信息從而適應嚴酷環(huán)境。這為研究生物在極端環(huán)境下的進化方向等提供了重要參考[51]。家蠅以人類和動物的排泄物為生，是包括肺結(jié)核、傷寒等多種疾病的載體?；蚪M測序分析發(fā)現(xiàn)家蠅基因組多樣性高，存在大量與免疫相關(guān)基因和特殊的解毒基因，揭示了家蠅對人類疾病產(chǎn)生免疫力和分解廢棄物的機制，這為害蟲綜合防治、廢棄物的分解利用和人類疾病的治療提供了一定的線索和思路[19]。地中海實蠅是一種毀滅性的果蔬害蟲，現(xiàn)已分布于80多個國家和地區(qū)，危害包括柑桔、蘋果、梨等水果和蔬菜在內(nèi)的250多種寄主，其基因組大小為479 Mb，基因組注釋獲得14,547個基因，有1608個進化的新基因。黑腹果蠅、家蠅和地中海實蠅基因組比較分析，發(fā)現(xiàn)地中海實蠅多個基因、基因家族出現(xiàn)擴張現(xiàn)象，這可能是導致地中海實蠅具有較高的適應性和入侵性的原因[44]。

3 雙翅目昆蟲基因組中功能基因研究進展

3.1 細胞色素P450基因

P450酶系包括多功能氧化酶和細胞色素P450 ()單加氧酶。其功能高度多樣，包括合成昆蟲發(fā)育和繁殖所需的重要激素和化學代謝物質(zhì)，從而促進昆蟲對寄主植物的適應性和對環(huán)境中有毒物質(zhì)如殺蟲劑的解毒作用。黑腹果蠅細胞色素P450家族共鑒定出90個基因，分屬25個家族，其中和家族的成員最多，占P450基因總數(shù)的一半[32]。地中海實蠅細胞色素P450家族包含103個基因和9個假基因，相較于黑腹果蠅的88個基因和3個假基因，地中海實蠅細胞色素P450家族顯著擴張，主要集中于和基因家族，其擴張性卻低于家蠅和基因家族[44]。地中海實蠅家族由40個基因和4個假基因組成，是黑腹果蠅家族23個基因的幾乎兩倍。其中、和亞家族出現(xiàn)顯著擴張，包含14個基因、包含9個基因、包含5個基因[44]。這3個亞家族基因和雙翅目昆蟲殺蟲劑抗性相關(guān)，其中家族通過基因簇復制快速擴張[65]。另外，在地中海實蠅基因組中發(fā)現(xiàn)18個連續(xù)的基因形成一個基因簇(13個屬于亞家族)，其中基因的過表達和氯氟氰菊酯抗性相關(guān)[66]。在黑腹果蠅基因組中發(fā)現(xiàn)2個和9個連續(xù)的基因形成兩個基因簇。地中海實蠅基因家族出現(xiàn)復制表明其參與環(huán)境響應如細胞色素P450調(diào)控的抗性。家蠅和黑腹果蠅基因家族和殺蟲劑抗性相關(guān)[65]。此外，細胞色素P450家族還包含蛻皮激素合成途徑相關(guān)基因，在地中海實蠅基因組中發(fā)現(xiàn)4個P450基因()、()、()、()能夠活化蛻皮激素。

3.2 免疫相關(guān)基因

免疫反應包括黑化作用、吞噬作用、包埋、凝血和脂肪體合成抗菌肽和抗菌蛋白[67]。涉及病菌識別和防御反應的四條主要信號途徑是：Toll、IMD、JAK/STAT和JNK[68]。昆蟲主要通過模式識別受體(PRRs)和肽聚糖識別蛋白(PGRPs)家族基因識別細菌，革蘭氏陰性細菌結(jié)合蛋白(GNBPs)通過結(jié)合細菌配體從而激活免疫途徑[69~71]。黑腹果蠅基因組鑒定出379個假定的免疫基因，地中海實蠅基因組鑒定出413個假定的免疫基因，家蠅基因組鑒定出771個假定的免疫基因。家蠅基因組中免疫基因數(shù)量巨大、免疫識別和受體基因的拷貝數(shù)和基因多樣性顯著增加的原因可能和其生活在富含病原菌的環(huán)境相關(guān)[19]。家蠅免疫識別受體Nimrods和thioester- containing proteins (Teps)拷貝數(shù)出現(xiàn)顯著擴張。家蠅具有17個Nimrods蛋白、19個Teps蛋白。黑腹果蠅具有11個Nimrods蛋白、6個Teps蛋白。在已測序果蠅屬物種中，Nimrods基因家族的拷貝數(shù)差異較大[72]。由于地中海實蠅極其多樣的寄主選擇性導致其免疫基因數(shù)量較多，從而應對寄主和環(huán)境條件中多種多樣的病原菌[44]。革蘭氏陰性細菌和真菌誘導免疫響應因子基因激活Toll信號途徑，地中海實蠅由于在不同果實上產(chǎn)卵接觸到的真菌感染導致家族基因和Toll受體家族基因出現(xiàn)高度擴張。地中海實蠅有17個Toll受體家族基因，而黑腹果蠅和家蠅只有9個。基因活化所必需的絲氨酸蛋白酶基因家族在地中海實蠅中也出現(xiàn)顯著擴張，相較于黑腹果蠅的45個和家蠅的28個，地中海實蠅具有50個絲氨酸蛋白酶基因[44]。

3.3 性別決定和分化相關(guān)基因

地中海實蠅基因組已鑒定出35個直接或者間接參與性別決定和性別分化基因，其中25個基因包括()、()、()基因，6個性別特異剪切基因和4個基因具有軀體性別特異功能如劑量補償[44,73,74]。通過比較家蠅雌成蟲和雄成蟲基因的表達量，已鑒定出113個雄性偏向性表達基因和81個雌性偏向性表達基因[19]。而在黑腹果蠅中10%~20%的基因具有性別偏向性表達的特性，比家蠅觀察到的明顯增多[75,76]。近年來雙翅目昆蟲基因組測序很大一部分是關(guān)于性染色體差異的進化模式研究(表1)，而基于基因組測序的策略已鑒定出多種雄性性別決定因子。埃及伊蚊染色體性別決定系統(tǒng)缺少Y染色體，Hall等[77]基于雌雄基因組測序發(fā)現(xiàn)埃及伊蚊雄性決定因子基因位于1號染色體的非重組區(qū)域，處于性別決定級聯(lián)反應的頂端，通過調(diào)控下游基因mRNA前體雄性特異剪切和表達，促進雄性發(fā)育。Krzywinska等[78]對岡比亞按蚊雌雄胚胎基因序列比較，在Y染色體上鑒定出一個僅在雄性早期轉(zhuǎn)錄表達基因，發(fā)現(xiàn)調(diào)控基因的雄性特異剪切和表達，從而實現(xiàn)雄性發(fā)育。家蠅有一個與眾不同的多態(tài)性別決定系統(tǒng)，雄性攜帶一個顯性的雄性決定因子，這個因子可以位于X或者Y或者任意5條常染色體上。基于家蠅基因組序列信息，Sharma等[79]闡明其性別決定系統(tǒng)由雄性決定因子()的存在與否來決定。Meccariello等[80]通過對地中海實蠅雄蟲構(gòu)建長讀長基因組文庫，篩選出性別決定基本信號是位于Y染色體上的雄性決定因子--()基因，通過阻止合子中基因活化，導致基因進行雄性特異剪切，引起雄性發(fā)育。此外，基因作為雄性決定因子在雙翅目實蠅科其他物種如橄欖果實蠅和橘小實蠅()中也是Y染色體連接，且功能保守[80]。

4 雙翅目昆蟲比較基因組學研究進展

目前，基因組結(jié)構(gòu)、基因含量、共線性、染色體倒位和非編碼元件進化研究是比較基因組學研究的重要領(lǐng)域[39,81,82]。雙翅目昆蟲比較基因組學研究闡明了新基因的形成[83,84]、基因和基因組互作與調(diào)控[85]和基因組塑造昆蟲生物史[86,87]等分子生物學問題。利用種屬水平的系統(tǒng)發(fā)育比較基因組學，雙翅目昆蟲中基因家族的進化關(guān)系逐漸得到闡述。家蠅作為世界性的衛(wèi)生害蟲，由于其獨特的取食習性、長期暴露在殺蟲劑下以及與動物病原菌之間的互作，系統(tǒng)發(fā)育比較基因組學已證明其與生理和行為適應性相關(guān)的細胞色素P450基因家族、化學感受受體和氣味結(jié)合蛋白基因的拷貝數(shù)發(fā)生了顯著變化[57]。已有研究表明，按蚊屬基因組基因拷貝數(shù)的擴增和收縮比果蠅屬快5倍[19]。蚊科和果蠅科中數(shù)量巨大的高質(zhì)量基因組數(shù)據(jù)可用于小型調(diào)控元件如microRNA、piwi-interacting RNA、Aubergine和功能性小閱讀框(smORF)的鑒定和系統(tǒng)進化分析[88~91]。

雙翅目昆蟲比較基因組學為闡明昆蟲進化模式和機制、適應性和生理功能以及基因型和表型之間的聯(lián)系提供了一個很好的手段。通過比較岡比亞按蚊不同染色體間的系統(tǒng)進化分析模式，發(fā)現(xiàn)其基因組中存在大量基因滲入現(xiàn)象，這為解釋新形成物種之間常染色體至X染色體的基因轉(zhuǎn)移速率差異提供了新的證據(jù)[57]。比較基因組學為計算近緣物種種群動態(tài)、種群分類排序和基因滲入在塑造昆蟲遺傳差異性等方面提供一個完整的研究系統(tǒng)[92]。蚊子間比較基因組學對于了解病原菌傳播的基本生物學過程以及探索調(diào)控病媒昆蟲防治的遺傳機制具有越來越重要的價值[93,94]。根據(jù)果蠅科已測序基因組建立的系統(tǒng)發(fā)育進化樹已被用來研究種間基因、基因組、調(diào)控網(wǎng)絡、發(fā)育途徑和生態(tài)適應等分子生物學問題的進化框架[95,96]。目前，總共有30種果蠅科昆蟲完成基因組組裝，其中23種來自水果果蠅亞屬()，另外7種來自果蠅亞屬()。果蠅科昆蟲間的比較基因組學有助于闡明DNA結(jié)合蛋白的基因調(diào)控機制，并鑒定出塑造雙翅目發(fā)育、行為和生理過程的保守直系同源調(diào)控基因結(jié)構(gòu)[97,98]。

雙翅目昆蟲功能基因組學和比較基因組學是研究昆蟲與植物互作的重要手段。植物寄生性麥廮蠅的基因組研究表明，有多種基因產(chǎn)物充當效應蛋白抑制植物防御，并調(diào)節(jié)宿主細胞誘導植物產(chǎn)生五倍子[45]。地中海實蠅功能基因組學鑒定出多種氣味結(jié)合蛋白、水通道蛋白和免疫反應基因，參與調(diào)控宿主植物適應性協(xié)同進化[44]。果蠅科昆蟲在發(fā)育進程中的植食性已出現(xiàn)多次進化，對斑翅果蠅()和黃果蠅()的比較基因組學研究發(fā)現(xiàn)，取食受損植物組織和取食正常植物組織前后會導致基因表達出現(xiàn)顯著性變化，主要包括與營養(yǎng)、規(guī)避植物防御和寄主定位相關(guān)基因的表達[99~101]。鑒于雙翅目昆蟲測序成本相對較低，大量果蠅科和蚊子種群基因組測序工作得以完成。果蠅科種群基因組計劃和果蠅基因參考圖譜是研究定量遺傳學的重要參考文庫，可獲得和測定特定品系的定量表型，并可鑒定其與先前基因組序列的關(guān)聯(lián)性[53~55]。利用DPGP已實現(xiàn)果蠅科昆蟲48種定量表型的遺傳學分析[42]。此外，雙翅目昆蟲具有高豐度和高耐受的染色體內(nèi)倒位現(xiàn)象，擬暗果蠅() 54個種群基因組學研究對3號染色體倒位多態(tài)性進行了鑒定[38]。對分布在非洲的765種岡比亞按蚊和個體進行測序發(fā)現(xiàn)，相較于黑腹果蠅0.5%的個體多態(tài)性和人類0.5%個體多態(tài)性，蚊子個體多態(tài)性為3%[102]。岡比亞按蚊種群基因組測序不僅推動了某些假定基因驅(qū)動(gene drive)的應用，還鑒定出遠距離基因漂流現(xiàn)象和物種間基因滲入與抗性等位基因的傳播有關(guān)。

5 結(jié)語與展望

目前雖然有大量雙翅目昆蟲完成基因組測序工作，但是測序樣本范圍極度失衡，已有基因組主要集中在果蠅科和蚊科，雙翅目其它科物種基因組測序還比較缺乏，許多常見科中的昆蟲尚未進行測序[103]。首先，通過實驗室飼養(yǎng)、區(qū)域生物調(diào)查合作和全球基因組計劃等可以實現(xiàn)雙翅目昆蟲基因組測序樣本的多樣化。雙翅目中取食習性和行為習性多樣的物種或者模式物種可繼續(xù)充當未來基因組測序工作的主要對象。眼蕈蚊(Sciaridae)就是其中一個很好的候選對象：多數(shù)眼蕈蚊是腐生或以真菌為食，但少數(shù)也能侵入活體植物組織。因而眼蕈蚊是研究發(fā)育調(diào)控基因擴增、性別決定、細胞凋亡、免疫以及染色體結(jié)構(gòu)多態(tài)性遺傳機制的模式物種[104]。對雙翅目昆蟲生理、生態(tài)或行為特征具有差異性的近緣物種進行基因組測序，能有效闡明昆蟲生物適應的遺傳和分子機制。其次，食蚜蠅科(Syrphidae)、蚤蠅科(Phoridae)、稈蠅科(Chloropidae)和家蠅科(Muscidae)昆蟲有植食性、寄生性和食真菌性等多種食性，而麗蠅科(Calliphoridae)、麻蠅科(Sarcophagidae)、家蠅科(Muscidae)、虱蠅科(Hippoboscidae)和狂蠅科(Oestridae)昆蟲具有哺乳動物或鳥類寄生性和無脊椎動物寄生性等。這些昆蟲的比較基因組學研究將有助于闡明雙翅目昆蟲適應性的關(guān)鍵遺傳調(diào)控因子。而對雙翅目中醫(yī)學重要性物種進行基因組測序?qū)⒂兄诮沂疚蜅⒌亓曅赞D(zhuǎn)變等一系列行為的遺傳學基礎。蚋科(Simuliidae)昆蟲刺吸人畜的血液，是人畜蟠尾絲蟲病的傳播媒介，然而蚋科尚無完整的基因組序列信息。最后，寄生昆蟲、傳粉昆蟲和捕食昆蟲基因組信息也極其缺乏。棲息地或寄主選擇具有差異性的物種間的比較基因組學研究將揭示雙翅目昆蟲寄主?；?、寄主尋找和規(guī)避寄主免疫系統(tǒng)的協(xié)同進化模式。將來對雙翅目更多科昆蟲進行基因組測序是了解雙翅目昆蟲基因和基因組，以及基因組功能如性染色體進化和多樣性的重要手段[33]。因此，全基因組測序、功能基因組學、進化生物學、比較基因組學、生物信息學分析等技術(shù)是推動雙翅目昆蟲基因組學在害蟲防治、資源昆蟲利用、藥物靶點開發(fā)及進化生物學等方面應用的重要手段[105~109]。

[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., 2011, 108(14): 5690–5695.

[3] Bertone MA, Courtney GW, Wiegmann BM. Phylo-genetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes., 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., 2005, 217–273.

[5] Ssymank A, Kearns CA, Pape T, Thompson FC. Pollinating flies (Diptera): A major contribution to plant diversity and agricultural production., 2008, 9(1–2): 86–89.

[6] Wiens JJ, Lapoint RT, Whiteman NK. Herbivory increases diversification across insect clades., 2015, 6(1): 8370–8370.

[7] Vicoso B, Bachtrog D. Numerous transitions of sex chromosomes in Diptera., 2015, 13(4): e1002078.

[8] Dikow RB, Frandsen PB, Turcatel M, Dikow T. Genomic and transcriptomic resources for assassin flies including the complete genome sequence of(Insecta: Diptera: Asilidae) and 16 rep-resentative transcriptomes., 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: Chromosomal, gene, and cis-element evolu-tion., 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. Thegene disruption project: progress using transposons with distinctive site specificities., 2011, 188(3): 731–743.

[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., 2014, 196(4): 961–971.

[12] Xue ZY, Wu MH, Wen KJ, Ren MD, Long L, Zhang XD, Gao GJ. CRISPR/Cas9 mediates efficient conditional mutagenesis in., 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., 2012, 2(4): 1014–1024.

[14] Geib SM, Calla B, Hall B, Hou SB, Manoukis NC. Characterizing the developmental transcriptome of the oriental fruit fly,(Diptera: Tephritidae) through comparative genomic analysis withutilizing modENCODE datasets., 2014, 15(1): 942–942.

[15] Gr?nke S, Clarke DF, Broughton S, Andrews TD, Partridge L. Molecular evolution and functional charac-terization of Drosophila insulin-like peptides., 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-widescreen for heat nociception identifiesas an evolutionarily conserved pain gene., 2010, 143(4): 628–638.

[17] Mahajan S, Bachtrog D. Convergent evolution of Y chromosome gene content in flies., 2017, 8(1): 785–785.

[18] Dermauw W, Van Leeuwen T. The ABC gene family in arthropods: Comparative genomics and role in insec-ticide transport and resistance., 2014, 45: 89–110.

[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,L., a global vector of diseases with adaptations to a septic environment., 2014, 15(10): 466–466.

[20] Groen SC, Whiteman NK. Usingto study the evolution of herbivory and diet specialization., 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., 2016, 25(5): 1157–1174.

[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 inand the genomic basis of chemical-ecological adaptation in., 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., 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, Asp?ck U, Asp?ck H, Bartel D, Blanke A, Berger S, B?hm 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., 2014, 346(6210): 763–767.

[25] Kutty SN, Wong WH, Meusemann K, Meier R, Cranston P. A phylogenomic analysis of(Diptera) resolves the relationships among the eight constituent families., 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., 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 ofestablishes a platform for mosquito comparative genomics., 2010, 330(6000): 86–88.

[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 formosquitoes in Papua New Guinea., 2015, 24(6): 1263–1274.

[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 thegenome using Hi-C yields chromosome-length scaffolds., 2017, 356(6333): 92–95.

[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., 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, Sim?o 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., 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., 2000, 287(5461): 2185–2195.

[33] Zhou Q, Bachtrog D. Sex-specific adaptation drives early sex chromosome evolution in., 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 themodENCODE transcriptome annotation., 2014, 24(7): 1209–1223.

[35] Sanchez-Flores A, Pe?aloza F, Carpinteyro-Ponce J, Nazario-Yepiz NO, Abreu-Goodger C, Machado CA, Markow TA. Genome evolution in three species of cactophilic., 2016, 6(10): 3097–3105.

[36] Khanna R, Mohanty S. Whole genome sequence resource of Indian., 2017, 17(3): 557–564.

[37] Mohanty S, Khanna R. Genome-wide comparative analysis of four Indianspecies., 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., 2017, 26(23): 6539–6562.

[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 thephylogeny., 2007, 450(7167): 203–218.

[40] Lack JB, Lange JD, Tang AD, Corbett-Detig RB, Pool JE. A thousand fly genomes: an expandedgenome nexus., 2016, 33(12): 3308–3313.

[41] Stanley CE, Kulathinal RJ. flyDIVaS: A comparative genomics resource fordivergence and selection., 2016, 6(8): 2355– 2363.

[42] Mackay TFC, Huang W. Charting the genotype- phenotype map: lessons from thegenetic reference panel., 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.genome unlocks parasitic fly biology to underpin future interventions., 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, Ure?a E, Vlachos IS, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM. The whole genome sequence of the Mediterranean fruit fly,(Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species., 2016, 17(1): 192.

[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, L?fstedt 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., 2015, 25(5): 613–620.

[46] Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Bj?rk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes., 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., 2016, 540(7631): 69–73.

[48] Andere AA, Platt RN, Ray DA, Picard CJ. Genome sequence ofMeigen (Diptera: Calli-phoridae): implications for medical, veterinary and forensic research., 2016, 17(1): 842.

[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 (): vector of African trypanosomiasis., 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(Phoridae)., 2009, 10: 382.

[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., 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, a major arbovirus vector., 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 205genetic reference panel lines., 2014, 24(7): 1193–1208.

[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 ofquantitative traits., 2012, 109(39): 15553–15559.

[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. Thegenetic reference panel., 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 thephylogeny., 2012, 29(11): 3459–3473.

[57] Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catte-ruccia F, Kakani EG. Extensive introgression in a malaria vector species complex revealed by phylogenomics., 2015, 347(6217): 1258524–1258524.

[58] Savard J, Tautz D, Lercher MJ. Genome-wide accelera-tion of protein evolution in flies (Diptera)., 2006, 6(1): 7–7.

[59] Zdobnov EM, Bork P. Quantification of insect genome divergence., 2007, 23(1): 16–20.

[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 ofand., 2002, 298(5591): 149–159.

[61] Craddock EM, Gall JG, Jonas M. Hawaiiangenomes: size variation and evolutionary expansions., 2016, 144(1): 107–124.

[62] Elliott TA, Gregory TR. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content., 2015, 370(1678): 20140331.

[63] Bargues N, Lerat E. Evolutionary history of LTR-retrotransposons among 20species., 2017, 8(1): 7–7.

[64] Waterhouse RM. A maturing understanding of the composition of the insect gene repertoire., 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 ofand metabolic resistance mediated by P450 in a resistant strain., 2015, 71(9): 1281–1291.

[67] Lemaitre B, Hoffmann J. The host defense of., 2007, 25(1): 697–743.

[68] Boutros M, Agaisse H, Perrimon N. Sequential activation of signaling pathways during innate immune responses in., 2002, 3(5): 711–722.

[69] Kang DW, Liu G, Lundstr?m A, Gelius E, Steiner H. A peptidoglycan recognition protein in innate immunity conserved from insects to humans., 95(17): 10078–10082.

[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 incells., 275(42): 32721–32727.

[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,., 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., 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,., 2008, 9(1): 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 deveop-ment in the Mediterranean fruit fly,., 10(1): 12.

[75] Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B. Constraint and turnover in sex-biased gene expression in the genus., 2007, 450(7167): 233– 237.

[76] Gnad F, Parsch J. Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression., 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., 2015, 348(6240): 1268–1270.

[78] Krzywinska E, Dennison NJ, Lycett G, Krzywinski J. A maleness gene in the malaria mosquito., 2016, 353(6294): 67–69.

[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, a paralog of the generic splice factor gene., 2017, 356(6338): 642– 645.

[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, Mathio-poulos KD, Ragoussis J, Vitagliano L, Tu ZJ, Papa-thanos PA, Robinson MD, Saccone G.() orchestrates male sex determination in major agricultural fruit fly pests., 2019, 365(6460): 1457–1460.

[81] Von Grotthuss M, Ashburner M, Ranz JM. Fragile regions and not functional constraints predominate in shaping gene organization in the genus., 2010, 20(8): 1084–1096.

[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,., 2014, 15(9): 459.

[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., 2008, 18(9): 1446– 1455.

[84] Zhao L, Saelao P, Jones CD, Begun DJ. Origin and spread of de Novo genes inpopulations., 2014, 343(6172): 769–772.

[85] Mackay TFC. Epistasis and quantitative traits: using model organisms to study gene-gene interactions., 2014, 15(1): 22–33.

[86] Bhutkar A, Schaeffer SW, Russo S, Xu M, Smith TF, Gelbart WM. Chromosomal rearrangement inferred from comparisons of 12genomes., 2008, 179(3): 1657–1680.

[87] Corbett-Detig RB, Hartl DL. Population genomics of inversion polymorphisms in., 2012, 8(12): e1003056.

[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 12genomes using evolutionary signatures., 2007, 450(7167): 219–232.

[89] Ladoukakis ED, Pereira V, Magny EG, Eyre-Walker A, Couso JP. Hundreds of putatively functional small open reading frames in., 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., 2016, 8(3): 507–518.

[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 thegenus., 2018, 28(1): 52–65.

[92] Mallet J, Besansky N, Hahn MW. How reticulated are species?, 2016, 38(2): 140–149.

[93] Severson DW, Behura SK. Mosquito genomics: Progress and challenges., 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 parasiteand its anopheline vectors., 2017, 18(1): 205–205.

[95] Singh ND, Larracuente AM, Sackton TB, Clark AG. Comparative genomics on thephylogenetic tree., 2009, 40:459–480.

[96] Markow TA. The secret lives offlies., 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 sixspecies., 2011, 43(5): 414–420.

[98] Carl S, Russell S. Comparative genomics of transcription factor binding in. In: Edited by Raman C, Goldsmith MR, Agunbiade TA. Short Views on Insect Genomics and Proteomics.Springer International Pub-lishing, 2015.

[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., 2014, 31(9): 2441–2456.

[100] Goldman-Huertas B, Mitchell RF, Lapoint RT, Faucher CP, Hildebrand JG, Whiteman NK. Evolution of herbivory inlinked to loss of behaviors, antennal responses, odorant receptors, and ancestral diet., 2015, 112(10): 3026–3031.

[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,., 2016, 17(1): 648–648.

[102] Fontaine MC. Genetic diversity of the African malaria vector., 2017, 552(7683): 96–100.

[103] Wiegmann BM, Richards S. Genomes of Diptera., 2018, 25: 116–124.

[104] Simon CR, Siviero F, Monesi N. Beyond DNA puffs: What can we learn from studying sciarids?, 2016, 54(7): 361–378.

[105] Hou L, Zhan S, Zhou X, Li F, Wand XH. Advances in research on insect genomics in China., 2017, 54(5): 693–704.侯麗, 詹帥, 周欣, 李飛, 王憲輝. 中國昆蟲基因組學的研究進展. 應用昆蟲學報, 2017, 54(5): 693–704.

[106] Zhang CX. Current research status and prospects of genomes of insects important to agriculture in China., 2015, 48(17): 3454–3462.張傳溪. 中國農(nóng)業(yè)昆蟲基因組學研究概況與展望. 中國農(nóng)業(yè)科學, 2015, 48(17): 3454–3462.

[107] Ye GY, Fang Q. Entomological research in the genomic age., 2011, 48(6): 1531–1538.葉恭銀, 方琦. 基因組時代的昆蟲學研究. 應用昆蟲學報, 2011, 48(6): 1531–1538.

[108] Zhou H, Shen J. Research on functional genomics of agriculture insects: Review and prospect., 2017, 39(2): 239–248.周行, 沈杰. 農(nóng)業(yè)昆蟲的功能基因組學研究: 回顧與展望. 環(huán)境昆蟲學報, 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., 2017, 39(1): 1–18.尹傳林, 李美珍, 賀康, 丁思敏, 郭殿豪, 席羽, 李飛. 昆蟲基因組及數(shù)據(jù)庫研究進展. 環(huán)境昆蟲學報, 2017, 39(1): 1–18.

Progress on genome sequencing of Dipteran insects

Wei Peng, Mengjie Feng, Hao Chen, Baoyu Han

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 organismsand. 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.

Diptera; genome characteristics; functional genes; comparative genomics; phyletic evolution

2020-05-06;

2020-09-06

聯(lián)合國糧農(nóng)組織和國際原子能署項目(編號：D44003)，國家重點研發(fā)計劃項目(編號：2018YFC1604402)，浙江省重點研發(fā)計劃項目(編號：2020C02026)和浙江省基礎公益研究計劃項目(編號：LGN18C160006，LGN20C140005)資助[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), and the Fundamental and Public Welfare of Zhejiang Province of China (Nos. LGN18C160006, LGN20C140005)]

彭威，博士，講師，研究方向：昆蟲生物化學與分子生物學。E-mail: pengwei@cjlu.edu.cn

彭威。

韓寶瑜，博士，教授，研究方向：昆蟲化學生態(tài)學。E-mail: hanby15@163.com

10.16288/j.yczz.20-130

https://kns.cnki.net/kcms/detail/11.1913.R.20201021.1052.002.html

URI: 2020/10/22 11:48:10

(責任編委: 張蔚)