Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

doi:10.3389/fgene.2021.658619

IOCAS-IR > 实验海洋生物学重点实验室

	Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species
	Yuan, Jianbo 1,2,3; Zhang, Xiaojun 1,2,3; Li, Fuhua 1,2,3; Xiang, Jianhai1,2,3
	2021-05-03
发表期刊	FRONTIERS IN GENETICS
卷号	12 页码:12
通讯作者	Xiang, Jianhai(jhxiang@qdio.ac.cn)
摘要	Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.
关键词	penaeid shrimp genome genome assembly genomic characteristic whole genome duplication
DOI	10.3389/fgene.2021.658619
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[41876167] ; National Natural Science Foundation of China[31830100] ; National Key Research & Development Program of China[2018YFD0900103] ; National Key Research & Development Program of China[2018YFD0900404] ; Qingdao National Laboratory for Marine Science and Technology[MS2017NO04] ; China Agriculture Research system-48[CARS-48]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000651095300001
出版者	FRONTIERS MEDIA SA
引用统计	被引频次：11[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/337002/170965
专题	实验海洋生物学重点实验室
通讯作者	Xiang, Jianhai
作者单位	1.Chinese Acad Sci, Inst Oceanol, CAS 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 Mega Sci, Qingdao, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Yuan, Jianbo,Zhang, Xiaojun,Li, Fuhua,et al. Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species[J]. FRONTIERS IN GENETICS,2021,12:12.
APA	Yuan, Jianbo,Zhang, Xiaojun,Li, Fuhua,&Xiang, Jianhai.(2021).Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species.FRONTIERS IN GENETICS,12,12.
MLA	Yuan, Jianbo,et al."Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species".FRONTIERS IN GENETICS 12(2021):12.

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