油茶象甲Curculio chinensis基因组Survey测序分析

doi:10.11924/j.issn.1000-6850.casb2023-0607

摘要/Abstract

摘要：

油茶象甲Curculio chinensis Chevrolat是危害中国特有木本油料树种——油茶的专性蛀果害虫，也是中国林业危险性有害生物之一，在中国不同油茶产区均有分布，对油茶的为害呈加重趋势。为了深入研究其遗传基础和寄主适应性，确定适合鞘翅目象甲科基因组测序研究策略，首先采取Survey测序，之后做深度基因组测序和大规模种群测序。研究采用二代高通量测序技术(MGISEQ-2000)，测定了油茶象甲基因组大小，并估计该物种基因组的杂合度、重复率和GC含量。结果显示：油茶象甲基因组大小约为1356.82 Mb，测序深度达到50×；K-mer分析油茶象甲基因组虽然具有杂合峰，但杂合率较低，为1.20%；基因组重复序列含量约为77%。该研究结果对于揭示油茶象甲适应性进化具有重要意义，可为后续构建完整基因组和多种群基因组测序提供策略选择依据。

关键词: 油茶象甲, 鞘翅目, Survey测序, 杂合率, GC含量

Abstract:

The camellia weevil, Curculio chinensis Chevrolat, is a host-specific predator of the seeds of oil-tea camellia, endemic woody oil-bearing plant in China. It is one of the dangerous pests in Chinese forestry, and is widely distributed in different oil-tea camellia planting areas of China with increasing damage. In order to further study its genetic basis and host adaptability, and determine sequencing strategies that were suitable for genome sequencing of Curculionidae in Coleoptera, survey sequencing was first adopted to lay the foundation for further deep genome sequencing and large-scale population sequencing. In this study, reads from second-generation high-throughput sequencing technology (MGISEQ-2000 Pair-End sequencing platform) was used to determine the genome size of C. chinensis, and estimate the heterozygosity, repetition rate and GC content of the genome mass of this species. The results showed that the genome size of C. chinensis was about 1356.82 Mb, and the sequencing depth reached 50×. K-mer analysis showed that although there was a heterozygous peak in the C. chinensis genome, the heterozygous rate was as low as 1.20%. And the content of repeated sequences was about 77%. The results of this study are of great significance to reveal the adaptive evolution of Camellia weevil, and can provide a basis for the selection of strategies for the subsequent construction of a complete genome and multi-population genome sequencing.

Key words: Curculio chinensis, Coleoptera, survey sequencing, heterozygous rate, GC content

张丽, 吴佳茜, 曾萝琦, 刘惠, 汤小宇. 油茶象甲Curculio chinensis基因组Survey测序分析[J]. 中国农学通报, 2024, 40(17): 135-141.

ZHANG Li, WU Jiaxi, ZENG Luoqi, LIU Hui, TANG Xiaoyu. Genome Survey Analysis of Curculio chinensis (Coleoptera: Curculionidae)[J]. Chinese Agricultural Science Bulletin, 2024, 40(17): 135-141.

图/表 5

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样品编号	样品性状	体积/μL	Nanodrop检测				Qubit检测
样品编号	样品性状	体积/μL	浓度/(ng/μL)	260/280	260/230		浓度/(ng/μL)	总量/μg
CC	澄清透明	55	258	1.82	2.05		215	11.8

样品编号	样品性状	体积/μL	Nanodrop检测				Qubit检测
样品编号	样品性状	体积/μL	浓度/(ng/μL)	260/280	260/230		浓度/(ng/μL)	总量/μg
CC	澄清透明	55	258	1.82	2.05		215	11.8

科	种名	基因组大小/Mb	GC含量/%	杂合率/%	重复率/%	参考文献
葬甲科Silphidae	大红葬甲Nicrophorus vespilloides	195.3	\	\	12.85	[19]
天牛科Cerambycidae	光肩星天牛Anoplophora glabripennis	710	33.4	\	62.1	[30]
犀金龟科Dynastidae	蛀犀金龟Oryctes borbonicus	518	\	\	29.2	[20]
犀金龟科Dynastidae	椰蛀犀金龟Oryctes rhinoceros	377.36	34.9	\	32.7	[11]
叩甲科Elateridae	发光叩头甲Ignelater luminosus (Illier, 1807)	845	\	\	34.1	[25]
露尾甲科Nitidulidae	蜂巢小甲虫Aethina tumida	234	\	\	\	[21]
金龟科Scarabaeidae	白星花金龟Protaetia brevitarsis	751.1	\	2.35	51.82	[29]
金龟科Scarabaeidae	双叉犀金龟Trypoxylus dichotomus	636.27	35.11	2.09	57.45	[10]
萤科Lampyridae	胸窗萤Pyrocoelia pectoralis Olivier	760	\	\	44.88	[26]
	东部萤火虫Photinus pyralis	471	\	\	42.6	[25]
	平家萤Aquatica lateralis (Motshulsky, 1860)	902	\	\	19.8	[25]
芫菁科Meloidae	眼斑沟芫菁Hycleus cichorii	111.7	32.3	1.16	22.73	[22]
	大斑沟芫菁Hycleus phaleratus (Pallas, 1781)	106.7	\	0.99	13.47	[22]
	圆点斑芫菁Mylabris aulica	288.5	\	\	50.62	[23]
瓢虫科Coccinellidae	异色瓢虫Harmonia axyridis (Pallas, 1773)	423	\	\	\	[27]
	七星瓢虫Coccinella septempunctata	515	\	\	\	[27[
	龟纹瓢虫Propylea japonica (Thunberg, 1781)	803.9	\	\	71.33	[28]
长蠹科Bostrichidae	谷蠹Rhyzopertha dominica (Fab.)	479.1	35	\	\	[24]
叶甲科 Chrysomelidae	广聚萤叶甲Ophraella communa Lesage	774	31.9	\	58.2	[36]
	玉米根萤叶甲Diabrotica virgifera virgifera	2418	36.5	\	\	未发表
	四纹豆象Callosobruchus maculatus	1007.8	37.7	\	64	[40]
	柳兰叶甲Altica viridicyanea (Baly)	864.8	31.67	\	62.9	[37]
	小萤叶甲属种Galerucella pusilla	513.24	33.7	\	46.65	[39]
	Galerucella calmariensis	588.27	33.8	\	48.55	[39]
	Galerucella tenella	460.59	33.6	\	40.84	[39]
	双斑萤叶甲Monolepta hieroglyphica	2400	30.29	0.67	52.61	[38]
象甲科 Curculionidae (Scolytinae)	油茶象甲Curculio chinensis Chevrolat	1356.8	35.69	1.2	77
	中欧山松大小蠹Dendroctonus ponderosae （雄/雌）	224.8/223.7	33.5/36.4	\	20/23	[33,43]
	咖啡果小蠹Hypothenemus hampei (Ferrari, 1867)	162.6	29.3	\	\	[35]
	红脂大小蠹Dendroctonus valens	322.4	36.7	\	45.22	[34]
	红棕象甲Rhynchophorus ferrugineus	588.8	31.5	\	\	未发表
	棉铃象甲Anthonomus grandis grandi	703.6	32.13	\	57.42	[12]
	白菜籽龟象Ceutorhynchus assimilis	674.95	35.29	\	\	未发表
象甲科 Curculionidae (Scolytinae	光臀八齿小蠹Ips nitidus	231.4	35.2	\	\	未发表
	云杉八齿小蠹Ips typographus	236.8	35.2	\	\	未发表
	油棕象甲Elaeidobius kamerunicus Faust	269.63	31.7	\	\	未发表
	阿根廷茎象甲Listronotus bonariensis (Kuschel)	1112.44	31.3	\	69.17	[32]
	胡萝卜象甲Listronotus oregonensis	1293.3	30.9	\	\	未发表
	球背象甲Pachyrhynchus sulphureomaculatus	2051.39	33.76	\	76.4	[31]
	白松木蠹象Pissodes strobi	1509.35	37.1	\	\	未发表
	米象Sitophilus oryzae	770.57	32.9	\	\	未发表

科	种名	基因组大小/Mb	GC含量/%	杂合率/%	重复率/%	参考文献
葬甲科Silphidae	大红葬甲Nicrophorus vespilloides	195.3	\	\	12.85	[19]
天牛科Cerambycidae	光肩星天牛Anoplophora glabripennis	710	33.4	\	62.1	[30]
犀金龟科Dynastidae	蛀犀金龟Oryctes borbonicus	518	\	\	29.2	[20]
犀金龟科Dynastidae	椰蛀犀金龟Oryctes rhinoceros	377.36	34.9	\	32.7	[11]
叩甲科Elateridae	发光叩头甲Ignelater luminosus (Illier, 1807)	845	\	\	34.1	[25]
露尾甲科Nitidulidae	蜂巢小甲虫Aethina tumida	234	\	\	\	[21]
金龟科Scarabaeidae	白星花金龟Protaetia brevitarsis	751.1	\	2.35	51.82	[29]
金龟科Scarabaeidae	双叉犀金龟Trypoxylus dichotomus	636.27	35.11	2.09	57.45	[10]
萤科Lampyridae	胸窗萤Pyrocoelia pectoralis Olivier	760	\	\	44.88	[26]
	东部萤火虫Photinus pyralis	471	\	\	42.6	[25]
	平家萤Aquatica lateralis (Motshulsky, 1860)	902	\	\	19.8	[25]
芫菁科Meloidae	眼斑沟芫菁Hycleus cichorii	111.7	32.3	1.16	22.73	[22]
	大斑沟芫菁Hycleus phaleratus (Pallas, 1781)	106.7	\	0.99	13.47	[22]
	圆点斑芫菁Mylabris aulica	288.5	\	\	50.62	[23]
瓢虫科Coccinellidae	异色瓢虫Harmonia axyridis (Pallas, 1773)	423	\	\	\	[27]
	七星瓢虫Coccinella septempunctata	515	\	\	\	[27[
	龟纹瓢虫Propylea japonica (Thunberg, 1781)	803.9	\	\	71.33	[28]
长蠹科Bostrichidae	谷蠹Rhyzopertha dominica (Fab.)	479.1	35	\	\	[24]
叶甲科 Chrysomelidae	广聚萤叶甲Ophraella communa Lesage	774	31.9	\	58.2	[36]
	玉米根萤叶甲Diabrotica virgifera virgifera	2418	36.5	\	\	未发表
	四纹豆象Callosobruchus maculatus	1007.8	37.7	\	64	[40]
	柳兰叶甲Altica viridicyanea (Baly)	864.8	31.67	\	62.9	[37]
	小萤叶甲属种Galerucella pusilla	513.24	33.7	\	46.65	[39]
	Galerucella calmariensis	588.27	33.8	\	48.55	[39]
	Galerucella tenella	460.59	33.6	\	40.84	[39]
	双斑萤叶甲Monolepta hieroglyphica	2400	30.29	0.67	52.61	[38]
象甲科 Curculionidae (Scolytinae)	油茶象甲Curculio chinensis Chevrolat	1356.8	35.69	1.2	77
	中欧山松大小蠹Dendroctonus ponderosae （雄/雌）	224.8/223.7	33.5/36.4	\	20/23	[33,43]
	咖啡果小蠹Hypothenemus hampei (Ferrari, 1867)	162.6	29.3	\	\	[35]
	红脂大小蠹Dendroctonus valens	322.4	36.7	\	45.22	[34]
	红棕象甲Rhynchophorus ferrugineus	588.8	31.5	\	\	未发表
	棉铃象甲Anthonomus grandis grandi	703.6	32.13	\	57.42	[12]
	白菜籽龟象Ceutorhynchus assimilis	674.95	35.29	\	\	未发表
象甲科 Curculionidae (Scolytinae	光臀八齿小蠹Ips nitidus	231.4	35.2	\	\	未发表
	云杉八齿小蠹Ips typographus	236.8	35.2	\	\	未发表
	油棕象甲Elaeidobius kamerunicus Faust	269.63	31.7	\	\	未发表
	阿根廷茎象甲Listronotus bonariensis (Kuschel)	1112.44	31.3	\	69.17	[32]
	胡萝卜象甲Listronotus oregonensis	1293.3	30.9	\	\	未发表
	球背象甲Pachyrhynchus sulphureomaculatus	2051.39	33.76	\	76.4	[31]
	白松木蠹象Pissodes strobi	1509.35	37.1	\	\	未发表
	米象Sitophilus oryzae	770.57	32.9	\	\	未发表