SNP development from RNA-seq data in a nonmodel fish: How many individuals are needed for accurate allele frequency prediction?

Molecular Ecology Resources

Volumn 14, Issue 1, 2014, Pages 157-165

  Schunter, C ^a,b   Garza, J C ^c   Macpherson, E ^a   Pascual, M ^b  

^a CENTRE D ESTUDIS AVANÇATS DE BLANES CEAB CSIC   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

^c SOUTHWEST FISHERIES SCIENCE CENTER   (United States)

Author keywords

Minor allele frequency; Non model species; RNA seq; SNP development; Tripterygion delaisi

Indexed keywords

TRIPTERYGION DELAISI;

ANIMAL; ARTICLE; CHORDATA; CLASSIFICATION; GENE FREQUENCY; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; MEDITERRANEAN SEA; METHODOLOGY; MINOR ALLELE FREQUENCY; MOLECULAR BIOLOGY; NON-MODEL SPECIES; POPULATION GENETICS; RNA-SEQ; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; SNP DEVELOPMENT; TRIPTERYGION DELAISI;

MINOR ALLELE FREQUENCY; NON-MODEL SPECIES; RNA-SEQ; SNP DEVELOPMENT; TRIPTERYGION DELAISI;

ANIMALS; CHORDATA; GENE FREQUENCY; GENETICS, POPULATION; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MEDITERRANEAN SEA; MOLECULAR BIOLOGY; POLYMORPHISM, SINGLE NUCLEOTIDE; SAMPLE SIZE;

EID: 84890136905     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12155     Document Type: Article

References (39)

1. Altshuler D, Pollara VJ, Cowles CR et al. (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 407, 513-516.
2. Anderson EC, Garza JC (2006) The power of single-nucleotide polymorphisms for large-scale parentage inference. Genetics, 172, 2567-2582.
3. Barshis DJ, Ladner JT, Oliver TA, Seneca FO, Traylor-Knowles N, Palumbi SR (2013) Genomic basis for coral resilience to climate change. Proceedings of the National Academy of Sciences of the United States of America, 110, 1387-1392.
4. Baruch E, Weller JI (2008) Estimation of the number of SNP genetic markers required for parentage verification. Animal Genetics, 39, 474-479.
5. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution, 18, 249-256.
6. Carreras-Carbonell J, Macpherson E, Pascual M (2005) Rapid radiation and cryptic speciation in mediterranean triplefin blennies (Pisces: Tripterygiidae) combining multiple genes. Molecular Phylogenetics and Evolution, 37, 751-761.
7. Carreras-Carbonell J, Macpherson E, Pascual M (2006) Population structure within and between subspecies of the Mediterranean triplefin fish Tripterygion delaisi revealed by highly polymorphic microsatellite loci. Molecular Ecology, 15, 3527-3539.
8. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics (Oxford, England), 21, 3674-3676.
9. De Pristo MA, Banks E, Poplin R et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43, 491-498.
10. De Wit P, Palumbi SR (2012) Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation. Molecular Ecology, 21, 2884-2897.
11. De Wit P, Pespeni MH, Ladner JT et al. (2012) The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis. Molecular Ecology Resources, 12, 1058-1067.
12. Domingues VS, Almada VC, Santos RS, Brito A, Bernardi G (2007) Phylogeography and evolution of the triplefin Tripterygion delaisi (Pisces, Blennioidei). Marine Biology, 150, 509-519.
13. Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity, 107, 1-15.
14. Everett MV, Grau ED, Seeb JE (2011) Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome. Molecular Ecology Resources, 11(Suppl. 1), 93-108.
15. Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, Brookes AJ (2004) Complex SNP-related sequence variation in segmental genome duplications. Nature Genetics, 36, 861-866.
16. Gautier M, Gharbi K, Cezard T et al. (2012) The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology, 21, 3165-3178.
17. Grabherr MG, Haas BJ, Yassour M et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644-652.
18. Hauser L, Baird M, Hilborn R, Seeb LW, Seeb JE (2011) An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Molecular Ecology Resources, 11(Suppl. 1), 150-161.
19. Helyar SJ, Hemmer-Hansen J, Bekkevold D et al. (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, 11(Suppl. 1), 123-136.
20. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11(Suppl. 1), 117-122.
21. Jones FC, Chan YF, Schmutz J et al. (2012) A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Current Biology, 22, 83-90.
22. Jonge J, Videler JJ (1989) Differences between the reproductive biologies of Tripterygion tripteronotus and T. delaisi (Pisces, Perciformes, Tripterygiidae): the adaptive significance of an alternative mating strategy and a red instead of a yellow nuptial colour. Marine Biology, 100, 431-437.
23. Lamichhaney S, Martinez Barrio A, Rafati N et al. (2012) Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proceedings of the National Academy of Sciences of the United States of America, 109, 19345-19350.
24. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25, 1754-1760.
25. Li H, Handsaker B, Wysoker A et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England), 25, 2078-2079.
26. Li R, Fan W, Tian G et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
27. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nature Reviews Genetics, 12, 671-682.
28. Milano I, Babbucci M, Panitz F et al. (2011) Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLoS ONE, 6, e28008.
29. Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19, 208-216.
30. Olsen MT, Volny VH, Bérubé M et al. (2011) A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Arctic ringed seal (Pusa hispida hispida). Molecular Ecology Resources, 11(Suppl. 1), 9-19.
31. Picoult-Newberg L, Ideker TE, Pohl MG et al. (1999) Mining SNPs from EST databases. Genome Research, 9, 167-174.
32. Renaut S, Nolte AW, Bernatchez L (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology, 19(Suppl. 1), 115-131.
33. Rousset F (2008) GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.
34. Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE (2012) Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism. PLoS ONE, 7, e49018.
35. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1092 human genomes. Nature, 491, 56-65.
36. Thompson EA (1987) Parental and sib likelihoods in genealogy reconstruction. Biometrics, 43, 585-600.
37. Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genetics, Selection, Evolution, 34, 275-305.
38. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57-63.
39. Wirtz P (1978) The Behaviour of the Mediterranean Tripterygion Species (Pisces, Blennioidei). Zeitschrift fur Tierpsychologie, 48, 142-174.