EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)

doi:10.1007/s00343-012-1252-2

IOCAS-IR > 实验海洋生物学重点实验室

	EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)
	Liu Chengzhang 1; Wang Xia2 ; Xiang Jianhai1 ; Li Fuhua 1; Xiang, JH (reprint author), Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China.
	2012-09-01
发表期刊	CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY
ISSN	0254-4059
卷号	30 期号:5 页码:713-723
文章类型	Article
摘要	Pacific white shrimp has become a major aquaculture and fishery species worldwide. Although a large scale EST resource has been publicly available since 2008, the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure. In this study, a set of 155 411 expressed sequence tags (ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms (SNPs) were predicted, including 9 546 transitions, 5 124 transversions and 2 481 indels. Among the 7 298 SNP substitutions located in functionally annotated contigs, 58.4% (4 262) are non-synonymous SNPs capable of introducing amino acid mutations. Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding. Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous, suggesting negative selection. Distribution of non-synonymous to synonymous substitutions (Ka/Ks) ratio ranges from 0 to 4.01, (average 0.42, median 0.26), suggesting that the majority of the affected genes are under purifying selection. Enrichment analysis identified multiple gene ontology categories under positive or negative selection. Categories involved in innate immune response and male gamete generation are rich in positively selected genes, which is similar to reports in Drosophila and primates. This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species. The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.
关键词	Litopenaeus Vannamei Single Nucleotide Polymorphism (Snp) Expressed Sequence Tag (Est) Shrimp Population Genetics Adaptive Evolution Darwinian Selection
学科领域	Limnology ; Oceanography
DOI	10.1007/s00343-012-1252-2
URL	查看原文
收录类别	SCI
语种	英语
WOS记录号	WOS:000308357800001
引用统计	被引频次：12[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/337002/12323
专题	实验海洋生物学重点实验室
通讯作者	Xiang, JH (reprint author), Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China.
作者单位	1.Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China 2.NW A&F Univ, Coll Life Sci, Ctr Bioinformat, Yangling 712100, Peoples R China
第一作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Liu Chengzhang,Wang Xia,Xiang Jianhai,et al. EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)[J]. CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY,2012,30(5):713-723.
APA	Liu Chengzhang,Wang Xia,Xiang Jianhai,Li Fuhua,&Xiang, JH .(2012).EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei).CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY,30(5),713-723.
MLA	Liu Chengzhang,et al."EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)".CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY 30.5(2012):713-723.

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