双翅目昆虫基因组研究进展

doi:10.16288/j.yczz.20-130

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

• Review • Previous Articles Next Articles

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)

Abstract

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

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

Figures/Tables 1

Table 1

The Summary of Dipteran genome assemblies"

科名	物种名	基因组序列号	基因组大小(Mb)	Contig N50 (bp)	特点	参考文献
潜蝇科 (Agromyzidae)	Liriomyza trifolii	GCA_001014935.1	69.70	1816	班潜蝇性染色体差异的进化模式研究	[7]
食虫虻科 (Asilidae)	Holcocephala fusca	GCA_001015215.1	516.23	1778	性染色体差异的进化模式研究	[7]
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]

Table 1

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