SNP genotyping and population genomics from expressed sequences - Current advances and future possibilities

Molecular Ecology

Volumn 24, Issue 10, 2015, Pages 2310-2323

  De Wit, Pierre ^a   Pespeni, Melissa H ^b   Palumbi, Stephen R ^c  

^a GÖTEBORG UNIVERSITY   (Sweden)

^b UNIVERSITY OF VERMONT   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

genotyping; population genomics; RNA Seq; SNP discovery; transcriptome assembly

Indexed keywords

GENETIC MARKER;

GENE EXPRESSION PROFILING; GENE FREQUENCY; GENETIC MARKER; GENOMICS; GENOTYPING TECHNIQUE; POPULATION GENETICS; PROCEDURES; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

GENE EXPRESSION PROFILING; GENE FREQUENCY; GENETIC MARKERS; GENETICS, POPULATION; GENOMICS; GENOTYPING TECHNIQUES; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, RNA;

EID: 84928365478     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13165     Document Type: Review

References (107)

1. Amin S, Prentis PJ, Gilding EK, Pavasovic A, (2014) Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: A comparison of De novo assemblers. BMC Research Notes, 7, 488.
2. Andres JA, Larson EL, Bogdanowicz SM, Harrison RG, (2013) Patterns of transcriptome divergence in the male accessory gland of two closely related species of field crickets. Genetics, 193, 501-513.
3. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G, (2008) LOSITAN: A workbench to detect molecular adaptation based on a F(st)-outlier method. BMC Bioinformatics, 9, 323.
4. Ashrafi H, Hill T, Stoffel K, et al,. (2012) De novo assembly of the pepper transcriptome (Capsicum annuum): A benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics, 13, 571.
5. Bai X, Rivera-Vega L, Mamidala P, et al,. (2011) Transcriptomic signatures of ash (Fraxinus spp.) phloem. PLoS ONE, 6, e16368.
6. 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.
7. Bay RA, Palumbi SR, (2014) Multilocus adaptation associated with heat resistance in reef-building corals. Current Biology. Available online, doi: 10.1016/j.cub.2014.10.044.
8. Beaumont MA, Nichols RA, (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society B-Biological Sciences, 263, 1619-1626.
9. Borodina T, Adjaye J, Sultan M, (2011) A strand-specific library preparation protocol for RNA sequencing. In: Methods in Enzymology, Vol 500: Methods in Systems Biology (eds, Jameson D, Verma M, Westerhoff HV,), pp. 79-98. Academic Press, San Diego, California.
10. Brown CT, Howe A, Zhang Q, Pyrkosz AB, Brom TH, (2012) A reference-free algorithm for computational normalization of shotgun sequencing data. ArXiv arXiv, 1203, 1-18.
11. Cahais V, Gayral P, Tsagkogeorga G, et al,. (2012) Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Molecular Ecology Resources, 12, 834-845.
12. Catalan A, Hutter S, Parsch J, (2012) Population and sex differences in Drosophila melanogaster brain gene expression. BMC Genomics, 13, 1-12.
13. Charlesworth B, Nordborg M, Charlesworth D, (1997) The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genetics Research, 70, 155-174.
14. Chen S, Yang P, Jiang F, et al,. (2010) De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS ONE, 5, e15633.
15. Choi M, Scholl UI, Ji W, et al,. (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, 106, 19096-19101.
16. Crusoe MR, Edvenson G, Fish J, et al,. (2014) The khmer software package: enabling efficient sequence analysis. Figshare. doi: 10.6084/m9.figshare,979190.
17. Cui J, Wang H, Liu S, et al,. (2014) SNP discovery from transcriptome of the swimbladder of Takifugu rubripes. PLoS ONE, 9, e92502.
18. De Wit P, Palumbi SR, (2013) Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation. Molecular Ecology, 22, 2884-2897.
19. De Wit P, Rogers-Bennett L, Kudela RM, Palumbi SR, (2014) Forensic genomics as a novel tool for identifying the causes of mass mortality events. Nature Communications, 5, 3652.
20. Degner JF, Marioni JC, Pai AA, et al,. (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics, 25, 3207-3212.
21. DePristo 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.
22. Doyle SR, Griffith IS, Murphy NP, Strugnell JM, (2014) Low-coverage MiSeq next generation sequencing reveals the mitochondrial genome of the Eastern Rock Lobster, Sagmariasus verreauxi. Mitochondrial DNA. Available online, doi: 10.3109/19401736.2013.855921.
23. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M, (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics, 12, 317.
24. Foll M, Gaggiotti O, (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics, 180, 977-993.
25. Fos M, Domínguez MA, Latorre A, Moya A, (1990) Mitochondrial DNA evolution in experimental populations of Drosophila subobscura. Proceedings of the National Academy of Sciences of the United States of America, 87, 4198-4201.
26. Francis WR, Christianson LM, Kiko R, et al,. (2013) A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genomics, 14, 167.
27. Fraser HB, Hirsh AE, Wall DP, Eisen MB, (2004) Coevolution of gene expression among interacting proteins. Proceedings of the National Academy of Sciences of the United States of America, 101, 9033-9038.
28. Fraser HB, Moses AM, Schadt EE, (2010) Evidence for widespread adaptive evolution of gene expression in budding yeast. Proceedings of the National Academy of Sciences, 107, 2977-2982.
29. Gagnaire P-A, Normandeau E, Cote C, Hansen MM, Bernatchez L, (2012) The genetic consequences of spatially varying selection in the panmictic american eel (Anguilla rostrata). Genetics, 190, 725-736.
30. Gallardo-Escàrate C, Núñez-Acuña G, Valenzuela-Muñoz V, (2013) SNP discovery in the marine gastropod Concholepas concholepas by high-throughput transcriptome sequencing. Conservation Genetics Resources, 5, 1053-1054.
31. Gayral P, Melo-Ferreira J, Glémin S, et al,. (2013) Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap. PLoS Genetics, 9, e1003457.
32. 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.
33. Haas BJ, Papanicolaou A, Yassour M, et al,. (2014) De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with trinity. Nature Protocols, 8, 1-43.
34. Han B, Kang EY, Raychaudhuri S, de Bakker PIW, Eskin E, (2014a) Fast pairwise IBD association testing in genome-wide association studies. Bioinformatics, 30, 206-213.
35. Han E, Sinsheimer JS, Novembre J, (2014b) Characterizing bias in population genetic inferences from low-coverage sequencing data. Molecular Biology and Evolution, 31, 723-735.
36. Harper AL, Trick M, Higgins J, et al,. (2012) Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nature Biotechnology, 30, 798-802.
37. Helyar SJ, Limborg MT, Bekkevold D, et al,. (2012) SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus). PLoS ONE, 7, e42089.
38. Huh D, Paulson J, (2010) Non-genetic heterogeneity from random partitioning at cell division. Nature Genetics, 43, 95-100.
39. Jaramillo-Correa JP, Beaulieu J, Bousquet J, (2001) Contrasting evolutionary forces driving population structure at expressed sequence tag polymorphisms, allozymes and quantitative traits in white spruce. Molecular Ecology, 10, 2729-2740.
40. Jeukens J, Renaut S, St-Cyr J, Nolte AW, Bernatchez L, (2010) The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Molecular Ecology, 19, 5389-5403.
41. Jones FC, Grabherr MG, Chan YF, et al,. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484, 55-61.
42. Kim SY, Lohmueller KE, Albrechtsen A, et al,. (2011) Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics, 12, 231.
43. Kofler R, Betancourt AJ, Schloetterer C, (2012) Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genetics, 8, e1002487.
44. Konczal M, Koteja P, Stuglik MT, Radwan J, Babik W, (2013) Accuracy of allele frequency estimation using pooled RNA-Seq. Molecular Ecology Resources, 14, 381-392.
45. Koren S, Schatz MC, Walenz BP, et al,. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30, 693-700.
46. Krasileva KV, Buffalo V, Bailey P, et al,. (2013) Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biology, 14, R66.
47. Le Corre V, Kremer A, (2012) The genetic differentiation at quantitative trait loci under local adaptation. Molecular Ecology, 21, 1548-1566.
48. Leder EH, McCairns RJS, Leinonen T, et al,. (2015) The evolution and adaptive potential of transcriptional variation in sticklebacks-signatures of selection and widespread heritability. Molecular Biology and Evolution, 32, 674-689.
49. Leffler EM, Gao Z, Pfeifer S, et al,. (2013) Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science, 339, 1578-1582.
50. Lemay MA, Donnelly DJ, Russello MA, (2013) Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon. BMC Genomics, 14, 308.
51. Li W, Godzik A, (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
52. Li H, Handsaker B, Wysoker A, et al,. (2009) The sequence alignment/map format and sam tools. Bioinformatics (Oxford, England), 25, 2078-2079.
53. Limborg MT, Helyar SJ, de Bruyn M, et al,. (2012) Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus). Molecular Ecology, 21, 3686-3703.
54. Liu J, McCleland M, Stawiski EW, et al,. (2014) Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer. Nature Communications, 5, 3830.
55. Livaja M, Wang Y, Wieckhorst S, et al,. (2013) BSTA: A targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower. BMC Genomics, 14, 628.
56. Loire E, Chiari Y, Bernard A, et al,. (2013) Population genomics of the endangered giant Galapagos tortoise. Genome Biology, 14, R136.
57. Lõpez-Maury L, Marguerat S, Bähler J, (2008) Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nature Reviews Genetics, 9, 583-593.
58. Lotterhos KE, Whitlock MC, (2014) Evaluation of demographic history and neutral parameterization on the performance of F-ST outlier tests. Molecular Ecology, 23, 2178-2192.
59. Lunter G, Goodson M, (2011) Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research, 21, 936-939.
60. Macmanes MD, Eisen MB, (2013) Improving transcriptome assembly through error correction of high-throughput sequence reads. PeerJ, 1, e113.
61. Manel S, Joost S, Epperson BK, et al,. (2010) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19, 3760-3772.
62. Martin JA, Wang Z, (2011) Next-generation transcriptome assembly. Nature Reviews Genetics, 12, 671-682.
63. Martins NE, Faria VG, Nolte V, et al,. (2014) Host adaptation to viruses relies on few genes with different cross-resistance properties. Proceedings of the National Academy of Sciences of the United States of America, 111, 5938-5943.
64. McKenna A, Hanna M, Banks E, et al,. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297-1303.
65. Montes I, Conklin D, Albaina A, et al,. (2013) SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing. PLoS ONE, 8, e70051.
66. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, et al,. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature, 464, 773-777.
67. Narum SR, Hess JE, (2011) Comparison of FST outlier tests for SNP loci under selection. Molecular Ecology Resources, 11, 184-194.
68. Nielsen R, Paul JS, Albrechtsen A, Song YS, (2011) Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12, 443-451.
69. Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J, (2012) SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS ONE, 7, e37558.
70. O'Neil ST, Emrich SJ, (2013) Assessing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics, 14, 465.
71. O'Rawe J, Jiang T, Sun G, et al,. (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Medicine, 5, 28.
72. Parra G, Bradnam K, Korf I, (2007) cegma: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics, 23, 1061-1067.
73. Pespeni MH, Palumbi SR, (2013) Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic. Molecular Ecology, 22, 3580-3597.
74. Pespeni MH, Oliver TA, Manier MK, Palumbi SR, (2010) Restriction Site Tiling Analysis: Accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays. Genome Biology, 11, R44.
75. Pespeni MH, Garfield DA, Manier MK, Palumbi SR, (2012) Genome-wide polymorphisms show unexpected targets of natural selection. Proceedings of the Royal Society B-Biological Sciences, 279, 1412-1420.
76. Pespeni MH, Chan F, Menge BA, Palumbi SR, (2013a) Signs of adaptation to local pH conditions across an environmental mosaic in the California Current ecosystem. Integrative and Comparative Biology, 53, 857-870.
77. Pespeni MH, Sanford E, Gaylord B, et al,. (2013b) Evolutionary change during experimental ocean acidification. Proceedings of the National Academy of Sciences of the United States of America, 110, 6937-6942.
78. Pickrell JK, Marioni JC, Pai AA, et al,. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464, 768-772.
79. Pootakham W, Uthaipaisanwong P, Sangsrakru D, et al,. (2013) Development and characterization of single-nucleotide polymorphism markers from 454 transcriptome sequences in oil palm (Elaeis guineensis). Plant Breeding, 132, 711-717.
80. Remm M, Storm CEV, Sonnhammer ELL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology, 314, 1041-1052.
81. Renaut S, Nolte AW, Rogers SM, Derome N, Bernatchez L, (2011) SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along gradients of ecological speciation in lake whitefish species pairs (Coregonus spp.). Molecular Ecology, 20, 545-559.
82. Romiguier J, Gayral P, Ballenghien M, et al,. (2014) Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature, 515, 261-263.
83. Ross MG, Russ C, Costello M, et al,. (2013) Characterizing and measuring bias in sequence data. Genome Biology, 14, R51.
84. Salzberg SL, Phillippy AM, Zimin A, et al,. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research, 22, 557-567.
85. Savolainen O, Lascoux M, Merilä J, (2013) Ecological genomics of local adaptation. Nature Reviews Genetics, 14, 807-820.
86. Schlötterer C, Tobler R, Kofler R, Nolte V, (2014) Sequencing pools of individuals-mining genome-wide polymorphism data without big funding. Nature Reviews Genetics, 15, 749-763.
87. Schulz MH, Zerbino DR, Vingron M, Birney E, (2012) oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28, 1086-1092.
88. Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM, (2011) A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Research, 21, 1728-1737.
89. Smith-Unna RD, Boursnell C, Patro R, Hibberd JM, Kelly S, (2014) Transrate v1.0.0.beta2. doi: 10.5281/zenodo14897.
90. Stillman JH, Armstrong E, (2015) Genomics are transforming our understanding of responses to climate change. BioScience. Available online, doi: 10.1093/biosci/biu219.
91. Sultan M, Schulz MH, Richard H, et al,. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956-960.
92. Szeto CYY, Lin CH, Choi SC, et al,. (2014) Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA-microRNA regulatory network in nasopharyngeal carcinoma model systems. FEBS Open Bio, 4, 128-140.
93. Tatusov RL, Fedorova ND, Jackson JD, et al,. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
94. Teer JK, Mullikin JC, (2010) Exome sequencing: the sweet spot before whole genomes. Human Molecular Genetics. Available online, doi: 10.1093/hmg/ddq333.
95. Tsagkogeorga G, Cahais V, Galtier N, (2012) The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis. Genome Biology and Evolution, 4, 852-861.
96. Utturkar SM, Klingeman DM, Land ML, et al,. (2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics, 30, 2709-2716.
97. Valenzuela-Muñoz V, Araya-Garay JM, Gallardo-Escàrate C, (2013) SNP discovery and high resolution melting analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens. Marine Genomics, 10, 11-16.
98. Van Der Auwera GA, Carneiro MO, Hartl C, et al,. (2013) From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics, 11, 11.10.1-11.10.33.
99. Vera JC, Wheat CW, Fescemyer HW, et al,. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology, 17, 1636-1647.
100. Vijay N, Poelstra JW, Kuenstner A, Wolf JBW, (2013) Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology, 22, 620-634.
101. Wang ET, Sandberg R, Luo S, et al,. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
102. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews. Genetics, 10, 57-63.
103. West MAL, Kim K, Kliebenstein DJ, et al,. (2007) Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics, 175, 1441-1450.
104. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ, (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clinical Chemistry, 860, 853-860.
105. Yang X, Dorman KS, Aluru S, (2010) Reptile: representative tiling for short read error correction. Bioinformatics, 26, 2526-2533.
106. Zheng Q, Wang XJ, (2008) GOEAST: A web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Research, 36, W358-W363.
107. Zou F, Chai HS, Younkin CS, et al,. (2012) Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants. PLoS Genetics, 8, e1002707.