SNP discovery in the transcriptome of white pacific shrimp Litopenaeus vannamei by next generation sequencing

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Yu, Yang ^a,b   Wei, Jiankai ^a,b   Zhang, Xiaojun ^a   Liu, Jingwen ^a,b   Liu, Chengzhang ^a   Li, Fuhua ^a   Xiang, Jianhai ^a  

^a INSTITUTE OF OCEANOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; GENE FREQUENCY; GENETIC ANALYZER; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC LINKAGE; LARVAL STAGE; LITOPENAEUS VANNAMEI; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PREDICTION; RELIABILITY; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

ANIMALS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PENAEIDAE; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSCRIPTOME;

EID: 84900435837     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0087218     Document Type: Article

References (47)

1. Zhang L, Yang C, Zhang Y, Li L, Zhang X, et al. (2006) A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica 131: 37-49.
2. Alcivar-Warren A, Meehan-Meola D, Park SW, Xu Z, Delaney M, et al. (2007) ShrimpMap: A low-density, microsatellite-based linkage map of the pacific whiteleg shrimp, Litopenaeus vannamei: Identification of sex-linked markers in linkage group 4. Jounal of Shellfish Research 26: 1259-1277.
3. Du ZQ, Ciobanu DC, Onteru SK, Gorbach D, Mileham AJ, et al. (2010) A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. Animal Genetics 41: 286-294.
4. Perez F, Erazo C, Zhinaula M, Volckaert F, Calderon J (2004) A sex-specific linkage map of the white shrimp Penaeus (Litopenaeus) vannamei based on AFLP markers. Aquaculture 242: 105-118. (Pubitemid 39584087)
5. Glenn KL, Grapes L, Suwanasopee T, Harris DL, Li Y, et al. (2005) SNP analysis of AMY2 and CTSL genes in Litopenaeus vannamei and Penaeus monodon shrimp. Animal Genetics 36: 235-236. (Pubitemid 40802080)
6. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, et al. (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307: 1072-1079. (Pubitemid 40262106)
7. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447: 1087-1093.
8. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, et al. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445: 881-885.
9. Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
10. Matsunami H, Yu H, Xie W, Wang J, Xing Y, et al. (2011) Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP/SSR Markers. PloS ONE 6: e17595.
11. Hubert S, Higgins B, Borza T, Bowman S (2010) Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics 11: 191.
12. Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad KT, et al. (2008) Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection. BMC Genetics 9: 18.
13. Prudence M, Moal J, Boudry P, Daniel JY, Quere C, et al. (2006) An amylase gene polymorphism is associated with growth differences in the Pacific cupped oyster Crassostrea gigas. Animal Genetics 37: 348-351. (Pubitemid 44091659)
14. Nguyen MT, Barnes AC, Mather PB, Li YT, Lyons RE (2010) Single nucleotide polymorphisms in the actin and crustacean hyperglycemic hormone genes and their correlation with individual growth performance in giant freshwater prawn Macrobrachium rosenbergii. Aquaculture 301: 7-15.
15. Gorbach DM, Hu ZL, Du ZQ, Rothschild MF (2009) SNP discovery in Litopenaeus vannamei with a new computational pipeline. Animal Genetics 40: 106-109.
16. Ciobanu DC, Bastiaansen JW, Magrin J, Rocha JL, Jiang DH, et al. (2010) A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Animal Genetics 41: 39-47.
17. Liu CZ, Wang X, Xiang JH, Li FH (2012) EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp (Litopenaeus vannamei). Chinese Journal of Oceanology and Limnology 30: 713-723.
18. Helyar SJ, Limborg MT, Bekkevold D, Babbucci M, van Houdt J, et al. (2012) SNP Discovery Using Next Generation Transcriptomic Sequencing in Atlantic Herring (Clupea harengus). PloS ONE 7(8): e42089.
19. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. The Plant Journal 51: 910-918. (Pubitemid 47301664)
20. Garvin MR, Saitoh K, Gharrett AJ (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Molecular Ecology Resources 10: 915-934.
21. Liu S, Zhou Z, Lu J, Sun F, Wang S, et al. (2011) Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics 12: 53.
22. An HS, Byun SG, Kim YC, Lee JW, Myeong JI (2011) Wild and hatchery populations of Korean starry flounder (Platichthys stellatus) compared using microsatellite DNA markers. International Journal of Molecular Sciences 12: 9189-9202.
23. Sha Z, Wang S, Zhuang Z, Wang Q, Wang Q, et al. (2010) Generation and analysis of 10 000 ESTs from the half-smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers. Journal of Fish Biology 76: 1190-1204.
24. Fu BD, He SP (2012) Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing. DNA Research 19: 131-142.
25. Xu J, Ji PF, Zhao ZX, Zhang Y, Feng JX, et al. (2012) Genome-wide SNP discovery from transcriptome of four common carp strains. PloS ONE 7(10): e48140.
26. Moen T, Hayes B, Baranski M, Berg PR, Kjoglum S, et al. (2008) A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 9: 223.
27. Zeng DG, Chen XL, Xie DX, Zhao YZ, Yang CL, et al. (2013) Transcriptome analysis of pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Taura Syndrome Virus (TSV) experimental infection. PloS ONE 8(3): e58627.
28. Li CZ, Weng SP, Chen YG, Yu XQ, Lu L, et al. (2012) Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique. PloS ONE 7(10): e47442.
29. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
30. Li SH, Zhang XJ, Sun Z, Li FH, Xiang JH (2013) Transcriptome analysis on chinese shrimp Fenneropenaeus chinensis during WSSV acute infection. PloS ONE 8(3): e58627.
31. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29: 644-652.
32. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
33. Quinn EM, Cormican P, Kenny EM, Hill M, Anney R, et al. (2013) Development of strategies for SNP detection in RNA-Seq data: application to lymphoblastoid cell lines and evaluation using 1000 genomes data. PloS ONE 8(3): e58815.
34. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research 36: 3420-3435. (Pubitemid 351859009)
35. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research 35: W182-W185.
36. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29: 644-652.
37. Zakas C, Schult N, McHugh D, Jones KL, Wares JP (2012) Transcriptome analysis and SNP development can resolve population differentiation of Streblospio benedicti, a developmentally dimorphic marine annelid. PloS ONE 7 (2): e31613.
38. Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, et al. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5: 247-252. (Pubitemid 351325649)
39. Miller NJ, Sun J, Sappington TW (2012) High-throughput transcriptome sequencing for SNP and gene discovery in a moth. Environmental Entomology 41: 997-1007.
40. Zhang X, Zhang T, Zhao C, Zhang B, Liu C, et al. Research progress in sequencing of Litopenaeus vannamei. Seventh International Crustacean Congress, Qingdao, China Jun 20-25, 2010(Abstract), P361.
41. Zhang LS, Guo XM (2010) Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture 302: 124-129.
42. Leu JH, Chen SH, Wang YB, Chen YC, Su SY, et al. (2011) A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp. Marine Biotechnology 13: 608-621.
43. Tseng MC (2012) Evolution of microsatellite Loci of tropical and temperate anguilla eels. International Journal of Molecular Sciences 13: 4281-4294.
44. Vera M, Alvarez-Dios JA, Fernandez C, Bouza C, Vilas R, et al. (2013) Development and validation of single nucleotide polymorphisms (SNPs) markers from two transcriptome 454-runs of turbot (Scophthalmus maximus) using high-throughput genotyping. International Journal of Molecular Sciences 14: 5694-5711.
45. Chen R, Davydov EV, Sirota M, Butte AJ (2010) Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PloS ONE 5(10): e13574.
46. Miyamoto Y, Mabuchi A, Shi DQ, Kubo T, Takatori Y, et al. (2007) A functional polymorphism in the 5′ UTR of GDF5 is associated with susceptibility to osteoarthritis. Nature Genetics 39: 529-533. (Pubitemid 46514783)
47. Saunders MA, Liang H, Li WH (2007) Human polymorphism at microRNAs and microRNA target sites. Proceedings of the National Academy of Sciences of the United States of America 104: 3300-3305. (Pubitemid 46364154)