雙翅目昆蟲基因組研究進(jìn)展

彭威，馮蒙潔，陳皓，韓寶瑜

綜 述

雙翅目昆蟲基因組研究進(jìn)展

彭威，馮蒙潔，陳皓，韓寶瑜

中國計(jì)量大學(xué)，浙江省生物計(jì)量及檢驗(yàn)檢疫技術(shù)重點(diǎn)實(shí)驗(yàn)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(gè)基因組已完整測(cè)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(gè)種群基因組。比較基因組學(xué)闡明了雙翅目昆蟲的多種生物學(xué)問題，為基因組結(jié)構(gòu)變異、遺傳機(jī)制以及基因、物種、種群的進(jìn)化速率和進(jìn)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(duì)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(jià)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(xì)胞色素P450、免疫、性別決定和分化相關(guān)基因的研究進(jìn)展，對(duì)雙翅目昆蟲比較基因組學(xué)中的重大發(fā)現(xiàn)進(jìn)行了總結(jié)，以期在快速發(fā)展的基因組組學(xué)時(shí)代為其他物種進(jìn)行基因組測(cè)序提供指導(dǎo)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(chǔ)。

雙翅目昆蟲；基因組特性；功能基因；比較基因組學(xué)；系統(tǒng)進(jìn)化

昆蟲是動(dòng)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(jì)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(gè)屬，總計(jì)158,000個(gè)種，分為5個(gè)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(gè)總科，總計(jì)80,000個(gè)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(gè)科，習(xí)性多樣，包括植食性、寄生性、食真菌、哺乳動(dòng)物寄生性、蛆病、吸血以及幼蟲取食腐爛有機(jī)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(yīng)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(dòng)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(shí)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(dǎo)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(xí)性、取食習(xí)性和形態(tài)適應(yīng)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(shí)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(cè)序的物種。同時(shí)，非模式物種基因組測(cè)序物種的數(shù)量也在增加[7,8]。目前雙翅目昆蟲中有多達(dá)110個(gè)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(cè)序數(shù)量的穩(wěn)步增長(zhǎng)、以及系統(tǒng)發(fā)育基因組學(xué)和比較基因組學(xué)的發(fā)展為研究種間和種內(nèi)水平的昆蟲遺傳機(jī)制和進(jìn)化過程提供了新的視角。雙翅目昆蟲基因組測(cè)序樣本覆蓋率的增加為評(píng)估果蠅屬和蚊子外物種進(jìn)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(xué)和比較基因組學(xué)已經(jīng)在基因調(diào)控和修復(fù)[9~12]、發(fā)育[13,14]、神經(jīng)生物學(xué)[15,16]、性別決定[17]、昆蟲抗藥性[18,19]、營(yíng)養(yǎng)?；痆20]和生態(tài)適應(yīng)[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(cè)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(dòng)昆蟲基因組學(xué)的發(fā)展，從系統(tǒng)生物學(xué)的角度來解決昆蟲學(xué)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(xì)胞色素P450、免疫、性別決定和分化相關(guān)基因研究進(jìn)展，總結(jié)了雙翅目昆蟲比較基因組學(xué)中的重大發(fā)現(xiàn)，以期為了解雙翅目昆蟲多樣性、生物學(xué)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(jìn)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(jì)晚期，大約與其他主要的全變態(tài)昆蟲同時(shí)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(jìn)化的歷史進(jìn)程，對(duì)充分闡明雙翅目昆蟲生命進(jìn)化構(gòu)成了挑戰(zhàn)。但是系統(tǒng)進(jìn)化基因組學(xué)研究有助于促進(jìn)我們對(duì)雙翅目生命進(jìn)化的理解[1,25]。目前，雙翅目亞目已完成110個(gè)物種基因組測(cè)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(gè)物種基因組測(cè)序，鑒定了岡比亞按蚊吸血生理適應(yīng)性和免疫相關(guān)基因表達(dá)，為了解吸血性媒介昆蟲的生理適應(yīng)機(jī)制及瘧疾的發(fā)病機(jī)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(zhǎng)[29]；利用長(zhǎng)讀長(zhǎng)測(cè)序方法對(duì)白紋伊蚊()基因組重測(cè)序，發(fā)現(xiàn)其N50>3 Mb[30]；對(duì)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(jìng)爭(zhēng)基因的快速進(jìn)化[31]。(2)果蠅科：共完成33個(gè)物種基因組測(cè)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(jiǎn)單重復(fù)序列、中度重復(fù)元件和一些單拷貝DNA，鑒定了與DNA復(fù)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(duì)12種果蠅、、、、、、、、、、和基因組測(cè)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(duì)變色伏繞眼果蠅()等10中果蠅性染色體差異的進(jìn)化模式進(jìn)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(cè)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(xué)或農(nóng)業(yè)重要性物種的基因組測(cè)序可為廣大科研工作者探索潛在的害蟲防控機(jī)制提供重要參考。雙翅目農(nóng)業(yè)重要性物種基因組測(cè)序包括多種作物或果蔬害蟲，如小麥害蟲麥癭蠅和10種實(shí)蠅科(Tephri-tidae)害蟲，如地中海實(shí)蠅、橄欖果實(shí)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(cè)序工作具有極其重要的價(jià)值[43]。地中海實(shí)蠅基因組鑒定超過1800個(gè)與入侵和寄主適應(yīng)相關(guān)基因家族發(fā)生擴(kuò)張[44]；瓜實(shí)蠅()基因組篩選出多個(gè)用于害蟲防治研究的候選靶標(biāo)基因；鑒定了防治銅綠蠅的靶標(biāo)基因[43]；麥癭蚊基因組鑒定出426個(gè)效應(yīng)家族基因和2個(gè)抵御寄主植物抗性基因[45]。雙翅目醫(yī)學(xué)重要性物種基因組測(cè)序包括多種吸血媒介昆蟲的基因組，如沙蠅3個(gè)毛蠓科(Psychodidae)物種、采采蠅6個(gè)舌蠅科(Glossinidae)物種和螯蠅1個(gè)蠅科(Muscidae)物種；鑒定了搖蚊科唾液腺相關(guān)基因表達(dá)和蛋白激酶相關(guān)基因表達(dá)[46,47]；伏蠅()基因組可以應(yīng)用于法醫(yī)鑒定[48]；舌蠅科總共完成6個(gè)物種基因組測(cè)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(shí)別和效應(yīng)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(cè)[50]；由于難以獲取足夠高質(zhì)量長(zhǎng)須羅蛉()和巴氏白蛉()DNA，導(dǎo)致毛蠓科基因組測(cè)序困難。最近完成超過35個(gè)物種基因組測(cè)序工作顯著提高了雙翅目昆蟲非模式物種測(cè)序覆蓋率和基因組學(xué)及性染色體差異的進(jìn)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(zhǎng)足蠅科、果蠅科和、實(shí)蠅科橄欖果實(shí)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(cè)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(xué)分析的成功建立和發(fā)展，而且極大地推動(dòng)了國際合作組織對(duì)12種果蠅屬和16種按蚊屬雙翅目昆蟲的基因組測(cè)序和組裝工作[31,39]。果蠅科種群基因組計(jì)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(gè)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(gè)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(jìn)化跨度最近為24萬年前，最遠(yuǎn)為2200萬年前至5500萬年前之間[56]；按蚊屬物種分支進(jìn)化跨度最近為54萬年前，最遠(yuǎn)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(xué)揭示了雙翅目昆蟲基因組進(jìn)化速率顯著加快[58]，使得雙翅目昆蟲相對(duì)于其他昆蟲而言是名副其實(shí)的“長(zhǎng)枝”進(jìn)化物種。而蚊子和果蠅的比較基因組學(xué)表明這兩類昆蟲以顯著較大的速率從彼此分化出去，進(jìn)而進(jìn)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(gè)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(duì)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(fù)非編碼DNA的差異導(dǎo)致[62,63]。TEs不僅介導(dǎo)物種的進(jìn)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(jìn)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(gè)基因，致倦庫蚊基因組總共有18,955個(gè)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(gè)[51]，最多的是家蠅中的23,884個(gè)[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(cè)序發(fā)現(xiàn)其基因組規(guī)模高度簡(jiǎn)化，大約只包含9900萬個(gè)堿基對(duì)，基因組中重復(fù)的基因序列很少，但與代謝功能、生長(zhǎng)發(fā)育相關(guān)的基因卻足夠多。南極蠓在漫長(zhǎng)的進(jìn)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(yīng)嚴(yán)酷環(huán)境。這為研究生物在極端環(huán)境下的進(jìn)化方向等提供了重要參考[51]。家蠅以人類和動(dòng)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(cè)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(duì)人類疾病產(chǎn)生免疫力和分解廢棄物的機(jī)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(shí)蠅是一種毀滅性的果蔬害蟲，現(xiàn)已分布于80多個(gè)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(gè)基因，有1608個(gè)進(jìn)化的新基因。黑腹果蠅、家蠅和地中海實(shí)蠅基因組比較分析，發(fā)現(xiàn)地中海實(shí)蠅多個(gè)基因、基因家族出現(xiàn)擴(kuò)張現(xiàn)象，這可能是導(dǎo)致地中海實(shí)蠅具有較高的適應(yīng)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(jìn)展

3.1 細(xì)胞色素P450基因

P450酶系包括多功能氧化酶和細(xì)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(xué)代謝物質(zhì)，從而促進(jìn)昆蟲對(duì)寄主植物的適應(yīng)性和對(duì)環(huán)境中有毒物質(zhì)如殺蟲劑的解毒作用。黑腹果蠅細(xì)胞色素P450家族共鑒定出90個(gè)基因，分屬25個(gè)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(shí)蠅細(xì)胞色素P450家族包含103個(gè)基因和9個(gè)假基因，相較于黑腹果蠅的88個(gè)基因和3個(gè)假基因，地中海實(shí)蠅細(xì)胞色素P450家族顯著擴(kuò)張，主要集中于和基因家族，其擴(kuò)張性卻低于家蠅和基因家族[44]。地中海實(shí)蠅家族由40個(gè)基因和4個(gè)假基因組成，是黑腹果蠅家族23個(gè)基因的幾乎兩倍。其中、和亞家族出現(xiàn)顯著擴(kuò)張，包含14個(gè)基因、包含9個(gè)基因、包含5個(gè)基因[44]。這3個(gè)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(fù)制快速擴(kuò)張[65]。另外，在地中海實(shí)蠅基因組中發(fā)現(xiàn)18個(gè)連續(xù)的基因形成一個(gè)基因簇(13個(gè)屬于亞家族)，其中基因的過表達(dá)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(gè)和9個(gè)連續(xù)的基因形成兩個(gè)基因簇。地中海實(shí)蠅基因家族出現(xiàn)復(fù)制表明其參與環(huán)境響應(yīng)如細(xì)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(xì)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(shí)蠅基因組中發(fā)現(xiàn)4個(gè)P450基因()、()、()、()能夠活化蛻皮激素。

3.2 免疫相關(guān)基因

免疫反應(yīng)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(shí)別和防御反應(yīng)的四條主要信號(hào)途徑是：Toll、IMD、JAK/STAT和JNK[68]。昆蟲主要通過模式識(shí)別受體(PRRs)和肽聚糖識(shí)別蛋白(PGRPs)家族基因識(shí)別細(xì)菌，革蘭氏陰性細(xì)菌結(jié)合蛋白(GNBPs)通過結(jié)合細(xì)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(gè)假定的免疫基因，地中海實(shí)蠅基因組鑒定出413個(gè)假定的免疫基因，家蠅基因組鑒定出771個(gè)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(shí)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(shí)別受體Nimrods和thioester- containing proteins (Teps)拷貝數(shù)出現(xiàn)顯著擴(kuò)張。家蠅具有17個(gè)Nimrods蛋白、19個(gè)Teps蛋白。黑腹果蠅具有11個(gè)Nimrods蛋白、6個(gè)Teps蛋白。在已測(cè)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(shí)蠅極其多樣的寄主選擇性導(dǎo)致其免疫基因數(shù)量較多，從而應(yīng)對(duì)寄主和環(huán)境條件中多種多樣的病原菌[44]。革蘭氏陰性細(xì)菌和真菌誘導(dǎo)免疫響應(yīng)因子基因激活Toll信號(hào)途徑，地中海實(shí)蠅由于在不同果實(shí)上產(chǎn)卵接觸到的真菌感染導(dǎo)致家族基因和Toll受體家族基因出現(xiàn)高度擴(kuò)張。地中海實(shí)蠅有17個(gè)Toll受體家族基因，而黑腹果蠅和家蠅只有9個(gè)?；蚧罨匦璧慕z氨酸蛋白酶基因家族在地中海實(shí)蠅中也出現(xiàn)顯著擴(kuò)張，相較于黑腹果蠅的45個(gè)和家蠅的28個(gè)，地中海實(shí)蠅具有50個(gè)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(shí)蠅基因組已鑒定出35個(gè)直接或者間接參與性別決定和性別分化基因，其中25個(gè)基因包括()、()、()基因，6個(gè)性別特異剪切基因和4個(gè)基因具有軀體性別特異功能如劑量補(bǔ)償[44,73,74]。通過比較家蠅雌成蟲和雄成蟲基因的表達(dá)量，已鑒定出113個(gè)雄性偏向性表達(dá)基因和81個(gè)雌性偏向性表達(dá)基因[19]。而在黑腹果蠅中10%~20%的基因具有性別偏向性表達(dá)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(cè)序很大一部分是關(guān)于性染色體差異的進(jìn)化模式研究(表1)，而基于基因組測(cè)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(cè)序發(fā)現(xiàn)埃及伊蚊雄性決定因子基因位于1號(hào)染色體的非重組區(qū)域，處于性別決定級(jí)聯(lián)反應(yīng)的頂端，通過調(diào)控下游基因mRNA前體雄性特異剪切和表達(dá)，促進(jìn)雄性發(fā)育。Krzywinska等[78]對(duì)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(gè)僅在雄性早期轉(zhuǎn)錄表達(dá)基因，發(fā)現(xiàn)調(diào)控基因的雄性特異剪切和表達(dá)，從而實(shí)現(xiàn)雄性發(fā)育。家蠅有一個(gè)與眾不同的多態(tài)性別決定系統(tǒng)，雄性攜帶一個(gè)顯性的雄性決定因子，這個(gè)因子可以位于X或者Y或者任意5條常染色體上?；诩蚁壔蚪M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(duì)地中海實(shí)蠅雄蟲構(gòu)建長(zhǎng)讀長(zhǎng)基因組文庫，篩選出性別決定基本信號(hào)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(dǎo)致基因進(jìn)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(shí)蠅科其他物種如橄欖果實(shí)蠅和橘小實(shí)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(xué)研究進(jìn)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(jìn)化研究是比較基因組學(xué)研究的重要領(lǐng)域[39,81,82]。雙翅目昆蟲比較基因組學(xué)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(xué)問題。利用種屬水平的系統(tǒng)發(fā)育比較基因組學(xué)，雙翅目昆蟲中基因家族的進(jìn)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(dú)特的取食習(xí)性、長(zhǎng)期暴露在殺蟲劑下以及與動(dòng)物病原菌之間的互作，系統(tǒng)發(fā)育比較基因組學(xué)已證明其與生理和行為適應(yīng)性相關(guān)的細(xì)胞色素P450基因家族、化學(xué)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(kuò)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(jìn)化分析[88~91]。

雙翅目昆蟲比較基因組學(xué)為闡明昆蟲進(jìn)化模式和機(jī)制、適應(yīng)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(gè)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(jìn)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(xué)為計(jì)算近緣物種種群動(dòng)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(gè)完整的研究系統(tǒng)[92]。蚊子間比較基因組學(xué)對(duì)于了解病原菌傳播的基本生物學(xué)過程以及探索調(diào)控病媒昆蟲防治的遺傳機(jī)制具有越來越重要的價(jià)值[93,94]。根據(jù)果蠅科已測(cè)序基因組建立的系統(tǒng)發(fā)育進(jìn)化樹已被用來研究種間基因、基因組、調(diào)控網(wǎng)絡(luò)、發(fā)育途徑和生態(tài)適應(yīng)等分子生物學(xué)問題的進(jìn)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(xué)有助于闡明DNA結(jié)合蛋白的基因調(diào)控機(jī)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(xué)和比較基因組學(xué)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(dāng)效應(yīng)蛋白抑制植物防御，并調(diào)節(jié)宿主細(xì)胞誘導(dǎo)植物產(chǎn)生五倍子[45]。地中海實(shí)蠅功能基因組學(xué)鑒定出多種氣味結(jié)合蛋白、水通道蛋白和免疫反應(yīng)基因，參與調(diào)控宿主植物適應(yīng)性協(xié)同進(jìn)化[44]。果蠅科昆蟲在發(fā)育進(jìn)程中的植食性已出現(xiàn)多次進(jìn)化，對(duì)斑翅果蠅()和黃果蠅()的比較基因組學(xué)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(huì)導(dǎo)致基因表達(dá)出現(xiàn)顯著性變化，主要包括與營(yíng)養(yǎng)、規(guī)避植物防御和寄主定位相關(guān)基因的表達(dá)[99~101]。鑒于雙翅目昆蟲測(cè)序成本相對(duì)較低，大量果蠅科和蚊子種群基因組測(cè)序工作得以完成。果蠅科種群基因組計(jì)劃和果蠅基因參考圖譜是研究定量遺傳學(xué)的重要參考文庫，可獲得和測(cè)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(shí)現(xiàn)果蠅科昆蟲48種定量表型的遺傳學(xué)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(gè)種群基因組學(xué)研究對(duì)3號(hào)染色體倒位多態(tài)性進(jìn)行了鑒定[38]。對(duì)分布在非洲的765種岡比亞按蚊和個(gè)體進(jìn)行測(cè)序發(fā)現(xiàn)，相較于黑腹果蠅0.5%的個(gè)體多態(tài)性和人類0.5%個(gè)體多態(tài)性，蚊子個(gè)體多態(tài)性為3%[102]。岡比亞按蚊種群基因組測(cè)序不僅推動(dòng)了某些假定基因驅(qū)動(dòng)(gene drive)的應(yīng)用，還鑒定出遠(yuǎn)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(cè)序工作，但是測(cè)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(cè)序還比較缺乏，許多常見科中的昆蟲尚未進(jìn)行測(cè)序[103]。首先，通過實(shí)驗(yàn)室飼養(yǎng)、區(qū)域生物調(diào)查合作和全球基因組計(jì)劃等可以實(shí)現(xiàn)雙翅目昆蟲基因組測(cè)序樣本的多樣化。雙翅目中取食習(xí)性和行為習(xí)性多樣的物種或者模式物種可繼續(xù)充當(dāng)未來基因組測(cè)序工作的主要對(duì)象。眼蕈蚊(Sciaridae)就是其中一個(gè)很好的候選對(duì)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(kuò)增、性別決定、細(xì)胞凋亡、免疫以及染色體結(jié)構(gòu)多態(tài)性遺傳機(jī)制的模式物種[104]。對(duì)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(jìn)行基因組測(cè)序，能有效闡明昆蟲生物適應(yīng)的遺傳和分子機(jī)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(dòng)物或鳥類寄生性和無脊椎動(dòng)物寄生性等。這些昆蟲的比較基因組學(xué)研究將有助于闡明雙翅目昆蟲適應(yīng)性的關(guān)鍵遺傳調(diào)控因子。而對(duì)雙翅目中醫(yī)學(xué)重要性物種進(jìn)行基因組測(cè)序?qū)⒂兄诮沂疚蜅⒌亓?xí)性轉(zhuǎn)變等一系列行為的遺傳學(xué)基礎(chǔ)。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(xué)研究將揭示雙翅目昆蟲寄主專化性、寄主尋找和規(guī)避寄主免疫系統(tǒng)的協(xié)同進(jìn)化模式。將來對(duì)雙翅目更多科昆蟲進(jìn)行基因組測(cè)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(jìn)化和多樣性的重要手段[33]。因此，全基因組測(cè)序、功能基因組學(xué)、進(jìn)化生物學(xué)、比較基因組學(xué)、生物信息學(xué)分析等技術(shù)是推動(dòng)雙翅目昆蟲基因組學(xué)在害蟲防治、資源昆蟲利用、藥物靶點(diǎn)開發(fā)及進(jìn)化生物學(xué)等方面應(yīng)用的重要手段[105~109]。

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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(xiàng)目(編號(hào)：D44003)，國家重點(diǎn)研發(fā)計(jì)劃項(xiàng)目(編號(hào)：2018YFC1604402)，浙江省重點(diǎn)研發(fā)計(jì)劃項(xiàng)目(編號(hào)：2020C02026)和浙江省基礎(chǔ)公益研究計(jì)劃項(xiàng)目(編號(hào)：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(xué)與分子生物學(xué)。E-mail: pengwei@cjlu.edu.cn

彭威。

韓寶瑜，博士，教授，研究方向：昆蟲化學(xué)生態(tài)學(xué)。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(zé)任編委: 張蔚)