Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas

doi:10.1111/1755-0998.13368

IOCAS-IR > 实验海洋生物学重点实验室

	Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas
	Qi, Haigang 1,2,3,5; Li, Li 1,3,4,5; Zhang, Guofan 1,2,3,5
	2021-04-18
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
页码	16
通讯作者	Li, Li([email protected]) ; Zhang, Guofan([email protected])
摘要	The Pacific oyster (Crassostrea gigas) is a widely distributed marine bivalve of great ecological and economic importance. In this study, we provide a high-quality chromosome-level genome assembled using Pacific Bioscience long reads and Hi-C-based and linkage-map-based scaffolding technologies and a high-resolution variation map constructed using large-scale resequencing analysis. The 586.8 Mb genome consists of 10 pseudochromosome sequences ranging from 38.6 to 78.9 Mb, containing 301 contigs with an N50 size of 3.1 Mb. A total of 30,078 protein-coding genes were predicted, of which 22,757 (75.7%) were high-reliability annotations supported by a homologous match to a curated protein in the SWISS-PROT database or transcript expression. Although a medium level of repeat components (57.2%) was detected, the genomic content of the segmental duplications reached 26.2%, which is the highest among the reported genomes. By whole genome resequencing analysis of 495 Pacific oysters, a comprehensive variation map was built, comprised of 4.78 million single nucleotide polymorphisms, 0.60 million short insertions and deletions, and 49,333 copy number variation regions. The structural variations can lead to an average interindividual genomic divergence of 0.21, indicating their crucial role in shaping the Pacific oyster genome diversity. The large amount of mosaic distributed repeat elements, small variations, and copy number variations indicate that the Pacific oyster is a diploid organism with an extremely high genomic complexity at the intra- and interindividual level. The genome and variation maps can improve our understanding of oyster genome diversity and enrich the resources for oyster molecular evolution, comparative genomics, and genetic research.
关键词	Crassostrea gigas genome Pacific oyster resequencing variation
DOI	10.1111/1755-0998.13368
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[41876169]; Major scientific and technological innovation projects in Shandong Province[2019JZZY010813]; Key Deployment Project of Centre for Ocean Mega-Research of Science, Chinese academy of science[COMS2019Q06]; Earmarked Fund for China Agriculture Research System[CARS-49]
WOS研究方向	Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS类目	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS记录号	WOS:000640876200001
出版者	WILEY
引用统计	被引频次：51[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/170499
专题	实验海洋生物学重点实验室
通讯作者	Li, Li; Zhang, Guofan
作者单位	1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, Peoples R China 4.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao, Peoples R China 5.Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao, Peoples R China
推荐引用方式 GB/T 7714	Qi, Haigang,Li, Li,Zhang, Guofan. Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas[J]. MOLECULAR ECOLOGY RESOURCES,2021:16.
APA	Qi, Haigang,Li, Li,&Zhang, Guofan.(2021).Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas.MOLECULAR ECOLOGY RESOURCES,16.
MLA	Qi, Haigang,et al."Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas".MOLECULAR ECOLOGY RESOURCES (2021):16.

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