Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas

doi:10.1093/gigascience/giad077

CORC > 海洋研究所 > 中国科学院海洋研究所 > 实验海洋生物学重点实验室

	Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas
	Qi, Haigang 5,6,7,8,9; Cong, Rihao 3,4,5,8,9; Wang, Yanjun 2; Li, Li 1,3,4,5,8; Zhang, Guofan 5,6,7,8,9
刊名	GIGASCIENCE
	2023-10-03
卷号	12 页码:14
关键词	oyster Crassostrea angulata Crassostrea gigas trio-binning haplotype-resolved genome
ISSN号	2047-217X
DOI	10.1093/gigascience/giad077
通讯作者	Li, Li(lili@qdio.ac.cn) ; Zhang, Guofan(gfzhang@qdio.ac.cn)
英文摘要	Background: The Portuguese oyster Crassostrea angulata and the Pacific oyster C. gigas are two major Crassostrea species that are naturally distributed along the Northwest Pacific coast and possess great ecological and economic value. Here, we report the construction and comparative analysis of the chromosome-level haplotype-resolved g enomes of the two oyster congeners. Findings: Based on a trio-binning strategy, the PacBio high-fidelity and Illumina Hi-C reads of the offspring of the hybrid cross C. angulata (male) x C. gigas (female) were partitioned and independently assembled to construct two chromosome-level fully phased genomes. The assembly size (contig N50 size, BUSCO completeness) of the two genomes were 582.4 M (12.8 M, 99.1%) and 606.4 M (5.46 M, 98.9%) for C. angulata and C. gigas, respectively, ranking at the top of mollusk genomes with high contiguity and integrity. The general features of the two genomes were highly similar, and 15,475 highly conserved ortholog gene pairs shared identical gene structures and similar genomic locations. Highly similar sequences can be primarily identified in the coding regions, whereas most noncoding regions and introns of genes in the same ortholog group contain substantial small genomic and/or structural variations. Based on population resequencing analysis, a total of 2,756 species-specific single-nucleotide polymorphisms and 1,088 genes possibly under selection were identified. Conclusions: This is the first report of trio-binned fully phased chromosome-level genomes in marine invertebrates. The study provides fundamental resources for the research on mollusk genetics, comparative genomics, and molecular evolution.
资助项目	National Key R&D Program of China[2022YFD2400301] ; National Natural Science Foundation of China[41876169] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA24030105] ; Key Research and Development Program of Shandong[2022LZGC015] ; China Agriculture Research System of MOF and MARA[CARS-49]
WOS关键词	ALIGNMENT ; DIVERGENCE ; ACCURATE ; SEARCH
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:001167990900001
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/184807]
专题	海洋研究所_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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Inst Oceanol, Marine Sci Data Ctr, Qingdao 266071, Peoples R China 3.Chinese Acad Sci, Innovat Seed Design, Wuhan 430072, Peoples R China 4.Chinese Acad Sci, Inst Hydrobiol, Key Lab Breeding Biotechnol & Sustainable Aquacul, Wuhan 430072, Peoples R China 5.Shandong Technol Innovat Ctr Oyster Seed Ind, Qingdao 266105, Peoples R China 6.Chinese Acad Sci, Inst Oceanol, Natl & Local Joint Engn Key Lab Ecol Mariculture, Qingdao 266071, Peoples R China 7.Laoshan Lab, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 8.Chinese Acad Sci, Inst Oceanol, Ctr Ocean Mega Sci, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 9.Chinese Acad Sci, CAS, Qingdao 266071, Peoples R China
推荐引用方式 GB/T 7714	Qi, Haigang,Cong, Rihao,Wang, Yanjun,et al. Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas[J]. GIGASCIENCE,2023,12:14.
APA	Qi, Haigang,Cong, Rihao,Wang, Yanjun,Li, Li,&Zhang, Guofan.(2023).Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas.GIGASCIENCE,12,14.
MLA	Qi, Haigang,et al."Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas".GIGASCIENCE 12(2023):14.