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

Your Location：

Home >

Browse articles >

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

OriginalPaper | Updated：2023-05-16

- EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)
- EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)
- 海洋湖沼学报（英文） 2012年30卷第5期页码：713-723
- Affiliations：
  
  1. Institute of Oceanology Chinese Academy of Sciences
  2. Center of Bioinformatics College of Life Science Northwest A&F University
- Author bio：
- Funds：
  
  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), and the Agricultural Science and Technology Achievements Transformation Funds Project (No. 2010GB24910700)
- DOI：10.1007/s00343-012-1252-2
  中图分类号：
- 网络首发：2012-09-05，
  
  纸质出版：2012
- Accepted：
Scan QR Code
EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)[J]. 海洋湖沼学报（英文）, 2012,30(5):713-723.

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
EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei)[J]. 海洋湖沼学报（英文）, 2012,30(5):713-723. DOI： 10.1007/s00343-012-1252-2.

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.

关键词

Keywords

references

Barker G, Batley J, O’sullivan H, Edwards K J, Edwards D. 2003. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics, 19(3): 421–422.

Brooker A L, Benzie J A H, Blair D, Versini J J. 2000. Population structure of the giant tiger prawn Penaeus monodon in Australian waters, determined using microsatellite markers. Marine Biology, 136(1): 149–157.

Bustamante C D, Fledel-Alon A, Williamson S, Nielsen R, Hubisz M T, Glanowski S, Tanenbaum D M, White T J, Sninsky J J, Hernandez R D, Civello D, Adams M D, Cargill M, Clark A G. 2005. Natural selection on proteincoding genes in the human genome. Nature, 437(7 062): 1 153–1 157.

Cheng T C, Xia Q Y, Qian J F, Liu C, Lin Y, Zha X F, Xiang Z H. 2004. Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao. Insect Biochemistry and Molecular Biology, 34(6): 523–530.

Ciobanu D C, Bastiaansen J W M, Magrin J, Rocha J L, Jiang D H, Yu N, Geiger B, Deeb N, Rocha D, Gong H, Kinghorn B P, Plastow G S, van der Steen H A M, Mileham A J. 2010. A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Animal Genetics, 41(1): 39–47.

Clark N L, Swanson W J. 2005. Pervasive adaptive evolution in primate seminal proteins. PLoS Genetics, 1(3): 335–342.

Du Z Q, Ciobanu D C, Onteru S K, Gorbach D, Mileham A J, Jaramillo G, Rothschild M F. 2010. A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. Animal Genetics, 41(3): 286–294.

Glenn K L, Grapes L, Suwanasopee T, Harris D L, Li Y, Wilson K, Rothschild M F. 2005. SNP analysis of AMY2 and CTSL genes in Litopenaeus vannamei and Penaeus monodon shrimp. Animal Genetics, 36(3): 235–236.

Gorbach D M, Hu Z L, Du Z Q, Rothschild M F. 2009. SNP discovery in Litopenaeus vannamei with a new computational pipeline. Animal Genetics, 40(1): 106–109.

Gray Y H M, Sved J A, Preston C R, Engels W R. 1998. Structure and associated mutational effects of the cysteine proteinase (CP1) gene of Drosophila melanogaster. Insect Molecular Biology, 7(3): 291–293.

Gross P S, Bartlett T C, Browdy C L, Chapman R W, Warr G W. 2001. Immune gene discovery by expressed sequence tag analysis of hemocytes and hepatopancreas in the Pacific White Shrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus. Developmental and Comparative Immunology, 25(7): 565–577.

Hamza I, Faisst A, Prohaska J, Chen J, Gruss P, Gitlin J D. 2001. The metallochaperone Atox1 plays a critical role in perinatal copper homeostasis. Proceedings of the National Academy of Sciences of the United States of America, 98(12): 6 848–6 852.

Hayes B, Laerdahl J K, Lien S, Moen T, Berg P, Hindar K, Davidson W S, Koop B F, Adzhubei A, Hoyheim B. 2007. An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture, 265(1–4): 82–90.

Hudson R R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18(2): 337–338.

Hung I H, Casareno R L B, Labesse G, Mathews F S, Gitlin J D. 1998. HAH1 is a copper-binding protein with distinct amino acid residues mediating copper homeostasis and antioxidant defense. Journal of Biological Chemistry, 273(3): 1 749–1 754.

Jiggins F M, Kim K W. 2007. A screen for immunity genes evolving under positive selection in Drosophila. Journal of Evolutionary Biology, 20(3): 965–970.

Jorde L B. 2000. Linkage disequilibrium and the search for complex disease genes. Genome Research, 10(10): 1 435–1 444.

Kimura M. 1977. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature, 267(19): 275–276.

Landegren U, Nilsson M, Kwok P Y. 1998. Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Research, 8(8): 769–776.

Meehan D, Xu Z K, Zuniga G, Alcivar-Warren A. 2003. High frequency and large number of polymorphic Microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei Crustacea: Decapoda. Marine Biotechnology, 5(4): 311–330.

Miyata T, Miyazawa S, Yasunaga T. 1979. Two types of amino acid substitutions in protein evolution. Journal of Molecular Evolution, 12(3): 219–236.

Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad K T, Fevolden S E, Berg P R, Lien S. 2008. Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. Bmc Genetics, 9: 18.

Moore S S, Whan V, Davis G P, Byrne K, Hetzel D J S, Preston N. 1999. The development and application of genetic markers for the Kuruma prawn Penaeus japonicus. Aquaculture, 173(1–4): 19–32.

Morin P A, Martien K K, Taylor B L. 2009. Assessing statistical power of SNPs for population structure and conservation studies. Molecular Ecology Resources, 9(1): 66–73.

Nei M. 2005. Selectionism and neutralism in molecular evolution. Molecular Biology and Evolution, 22(12): 2 318–2 342.

Nielsen R. 2000. Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics, 154(2): 931–942.

Nielsen R, Bustamante C, Clark A G, Glanowski S, Sackton T B, Hubisz M J, Fledel-Alon A, Tanenbaum D M, Civello D, White T J, Sninsky J J, Adams M D, Cargill M. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology, 3(6): 976–985.

Novaes E, Drost D R, Farmerie W G, Pappas G J, Grattapaglia D, Sederoff R R, Kirst M. 2008. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9(1): 312.

O’Leary N A, Trent H F, Robalino J, Peck M E T, McKillen D J, Gross P S. 2006. Analysis of multiple tissue-specific cDNA libraries from the Pacific whiteleg shrimp, Litopenaeus vannamei. Integrative and Comparative Biology, 46(6): 931–939.

Perler F, Efstratiadis A, Lomedico P, Gilbert W, Kolodner R, Dodgson J. 1980. The evolution of genes: the chicken preproinsulin gene. Cell, 20(2): 555–566.

Pertea G, Huang X Q, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J. 2003. TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19(5): 651–652.

Roth C, Liberles D A. 2006. A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biology, 6: 12.

Shapiro J A, Huang W, Zhang C H, Hubisz M J, Lu J, Turissini D A, Fang S, Wang H Y, Hudson R R, Nielsen R, Chen Z, Wu C I. 2007. Adaptive genic evolution in the Drosophila genomes. Proceedings of the National Academy of Sciences of the United States of America, 104(7): 2 271–2 276.

Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton J M. 2010. Gene mapping in the wild with SNPs: guidelines and future directions (vol. 136, p.97, 2009). Genetica, 138(4): 467–467.

Smith N G C, Eyre-Walker A. 2002. Adaptive protein evolution in Drosophila. Nature, 415(6 875): 1 022–1 024.

Swanson W J, Clark A G, Waldrip-Dail H M, Wolfner M F, Aquadro C F. 2001. Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 98(13): 7 375–7 379.

Syvanen A C. 2001. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Reviews Genetics, 2(12): 930–942.

Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences (American Mathematical Society), 17: 57–86.

Thornsberry J M, Goodman M M, Doebley J, Kresovich S, Nielsen D, Buckler E S. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics, 28(3): 286–289.

Voight B F, Kudaravalli S, Wen X Q, Pritchard J K. 2006. A map of recent positive selection in the human genome. PLoS Biology, 4(3): 446–458.

Williamson S H, Hubisz M J, Clark A G, Payseur B A, Bustamante C D, Nielsen R. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genetics, 3(6): 901–915.

Wilson K, Li Y T, Whan V, Lehnert S, Byrne K, Moore S, Pongsomboon S, Tassanakajon A, Rosenberg G, Ballment E, Fayazi Z, Swan J, Kenway M, Benzie J. 2002. Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism. Aquaculture, 204(3–4): 297–309.

Wolfner M F. 2002. The gifts that keep on giving: physiological functions and evolutionary dynamics of male seminal proteins in Drosophila. Heredity, 88: 85–93.

Wyban J. 2007. Domestication of pacific white shrimp revolutionizes aquaculture. Global Aquaculture Advocate, 10: 42–44.

Yang Z, Bielawski J P. 2000. Statistical methods for detecting molecular adaptation. Trends in Ecology & Evolution, 15(12): 496–503.

Yang Z H, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution, 17(1): 32–43.

Yu M, Cheng Y, Rothschild M F. 2006. SNP analysis of molting related genes in Penaeus monodon and Litopenaeus vannamei shrimp (Brief report). Archiv Fur Tierzucht — Archives of Animal Breeding, 49(4): 411–412.

Zeng D G, Chen X H, Li Y M, Peng M, Ma N, Jiang W M, Yang C L, Li M. 2008. Analysis of HSP70 in Litopenaeus vannamei and detection of SNPs. Journal of Crustacean Biology, 28(4): 727–730.

Zhang Z, Li J, Zhao X Q, Wang J, Wong G K S, Yu J. 2006. KaKs_calculator: calculating Ka and Ks through model selection and model averaging. Genomics, Proteomics & Bioinformatics, 4(4): 259–263.

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

Peritrophin-like protein from Litopenaeus vannamei (LvPT) involved in white spot syndrome virus (WSSV) infection in digestive tract challenged with reverse gavage

Effects of water temperature and dietary carbohydrate levels on growth and energy budget of juvenileLitopenaeus vannamei

Closed recirculating system for shrimp-mollusk polyculture

Regulation of water quality and growth characteristics of indoor raceway culture of Litopenaeus vannamei

Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta)