EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp(Litopenaeus vannamei)
文献类型：CNKI期刊论文
| 作者 | Liu CZ(柳承璋); Wang X(王霞) ; Xiang JH(相建海); Li FH(李富花)
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| 发表日期 | 2012-09-15 |
| 出处 | Chinese Journal of Oceanology and Limnology
 |
| 关键词 | Litopenaeus vannamei single nucleotide polymorphism(SNP) expressed sequence tag(EST) shrimp population genetics adaptive evolution Darwinian selection |
| 英文摘要 | 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. |
| 文献子类 | CNKI期刊论文 |
| 资助机构 | Supported by the Key Program of National Natural Science Foundation of China (No.30730071) ; the National High Technology R&D Program of China(863 Program)(No.2012AA10A404) ; the Agricultural Science and Technology Achievements Transformation Funds Project(No.2010GB24910700) |
| 卷 | v.30期:05页:3-13 |
| 语种 | 英文; |
| 分类号 | S917.4 |
| ISSN号 | 0254-4059 |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/191128]  |
| 专题 | 中国科学院海洋研究所 |
| 作者单位 | 1.InstituteofOceanology,ChineseAcademyofSciences 2.CenterofBioinformatics,CollegeofLifeScience,NorthwestA&FUniversity |
| 推荐引用方式 GB/T 7714 | Liu CZ,Wang X,Xiang JH,et al. EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp(Litopenaeus vannamei). 2012. |
入库方式： OAI收割
来源：海洋研究所
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