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

Chengzhang Liu; Xia Wang; Jianhai Xiang; Fuhua Li

doi:10.1007/s00343-012-1252-2

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

Updated：2023-05-16

- EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)
- Journal of Oceanology and Limnology Vol. 30, Issue 5, Pages: 713-723(2012)
- Affiliations：
  
  1. Institute of Oceanology Chinese Academy of Sciences
  2. Center of Bioinformatics College of Life Science Northwest A&F University
- Author bio：
- Funds：
- DOI：10.1007/s00343-012-1252-2
  CLC：
- Online First：05 September 2012，
  
  Published：2012
- Accepted：
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Liu, C., Wang, X., Xiang, J. et al. EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)., Chin. J. Ocean. Limnol. 30, 713–723 (2012). https://doi.org/10.1007/s00343-012-1252-2
DOI：

Liu, C., Wang, X., Xiang, J. et al. EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)., Chin. J. Ocean. Limnol. 30, 713–723 (2012). https://doi.org/10.1007/s00343-012-1252-2 DOI：

摘要

Abstract

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.

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