Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

Molecular Ecology Resources

Volumn 15, Issue 1, 2015, Pages 28-41

  Mastretta Yanes, A ^a   Arrigo, N ^b   Alvarez, N ^b   Jorgensen, T H ^c   Pinero D ^d   Emerson, B C ^a,e  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c AARHUS UNIVERSITY   (Denmark)

^d INSTITUTO DE ECOLOGÍA   (Mexico)

^e Island Ecology and Evolution Research Group Instituto de Productos Naturales y Agrobiología IPNA CSIC   (Mexico)

Author keywords

Stacks; de novo assembly; Error rate; Optimization; RAD sequencing; Replicates

Indexed keywords

BERBERIS;

BERBERIS; CLASSIFICATION; DIAGNOSTIC ERROR; DNA SEQUENCE; EVALUATION STUDY; GENETIC VARIABILITY; GENETICS; GENOTYPE; GENOTYPING TECHNIQUE; MEXICO; POPULATION GENETICS; PROCEDURES;

BERBERIS; DIAGNOSTIC ERRORS; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; GENOTYPING TECHNIQUES; MEXICO; SEQUENCE ANALYSIS, DNA;

EID: 84932109367     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12291     Document Type: Article

References (49)

1. Baird NA, Etter PD, Atwood TS et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3, e3376.
2. Baxter SW, Davey JW, Johnston JS et al. (2011) Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One, 6, e19315.
3. Bonin A, Bellemain E, Bronken Eidesen P et al. (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261-3273.
4. Buerkle CA, Gompert Z (2013) Population genomics based on low coverage sequencing: how low should we go? Molecular Ecology, 22, 3028-3035.
5. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1, 171-182.
6. Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140.
7. Chong Z, Ruan J, Wu C-I (2012) Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads. Bioinformatics, 28, 2732-2737.
8. Crawford LA, Koscinski D, Keyghobadi N (2012) A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research. Molecular Ecology, 21, 5911-5917.
9. Davey JW, Hohenlohe PA, Etter PD et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
10. Davey JW, Cezard T, Fuentes-Utrilla P et al. (2013) Special features of RAD sequencing data: implications for genotyping. Molecular Ecology, 22, 3151-3164.
11. Dou J, Zhao X, Fu X et al. (2012) Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions. Biology Direct, 7, 17.
12. Eaton DAR (2014) PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics, doi:10.1093/bioinformatics/btu121.
13. Gautier M, Foucaud J, Gharbi K et al. (2013a) Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping. Molecular Ecology, 22, 3766-3779.
14. Gautier M, Gharbi K, Cezard T et al. (2013b) The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology, 22, 3165-3178.
15. Gomes I, Collins A, Lonjou C et al. (1999) Hardy-Weinberg quality control. Annals of Human Genetics, 63, 535-538.
16. Gompert Z, Buerkle CA (2011) A hierarchical Bayesian model for next-generation population genomics. Genetics, 187, 903-917.
17. Grundemann D, Schomig E (1996) Protection of DNA during preparative agarose gel electrophoresis against damage induced by ultraviolet light. BioTechniques, 21, 898-903.
18. Hohenlohe PA, Catchen J, Cresko WA (2012) Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. Methods in Molecular Biology (Clifton, N.J.), 888, 235-260.
19. Johnson PLF, Slatkin M (2008) Accounting for bias from sequencing error in population genetic estimates. Molecular Biology and Evolution, 25, 199-206.
20. Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403-1405.
21. Jones JC, Fan S, Franchini P, Schartl M, Meyer A (2013) The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Molecular Ecology, 22, 2986-3001.
22. Li H, Handsaker B, Wysoker A et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
23. Loman NJ, Misra RV, Dallman TJ et al. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30, 434-439.
24. 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.
25. Meacham F, Boffelli D, Dhahbi J et al. (2011) Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics, 12, 451.
26. Miller CR, Joyce P, Waits LP (2002) Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics, 160, 357-366.
27. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
28. Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA (2013) Genotyping-by-sequencing in ecological and conservation genomics. Molecular Ecology, 22, 2841-2847.
29. Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12, 443-451.
30. Paradis E, Claude J, Strimmer K (2004) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics, 20, 289-290.
31. Parchman TL, Gompert Z, Mudge J et al. (2012) Genome-wide association genetics of an adaptive trait in lodgepole pine. Molecular Ecology, 21, 2991-3005.
32. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One, 7, e37135.
33. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nature Reviews. Genetics, 6, 847-859.
34. Pool JE, Hellmann I, Jensen JD, Nielsen R (2010) Population genetic inference from genomic sequence variation. Genome Research, 20, 291-300.
35. Price DL, Casler MD (2012) Simple regression models as a threshold for selecting AFLP loci with reduced error rates. BMC Bioinformatics, 13, 268.
36. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
37. R Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
38. Richards PM, Liu MM, Lowe N et al. (2013) RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene. Molecular Ecology, 22, 3077-3089.
39. Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Research, 38, D234-D236.
40. Rounsaville TJ, Ranney TG (2010) Ploidy levels and genome sizes of Berberis L. and Mahonia Nutt. species, hybrids, and cultivars. HortScience, 45, 1029-1033.
41. Taberlet P, Griffin S, Goossens B et al. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 24, 3189-3194.
42. Urbanek S (2011) Multicore: Parallel Processing of R Code on Machines with Multiple Cores or CPUs. R package version 0.1-7. Available from http://CRAN.R-roject.org/package=multicore.
43. Vázquez-Lobo A (1996) Filogenia de hongos endófitos del género Pinus: Implementación de técnicas moleculares y resultados preliminares. Sc. Bach. Dissertation, Facultad de Ciencias, Universidad Nacional Autónoma de México, México.
44. Warnes GR, Bolker B, Lumley T (2013) gtools: Various R Programming Tools. R package version 2.7.1. Available from http://CRAN.R-project.org/package=gtools.
45. Wickham H (2012) stringr: Make It Easier to Work with Strings. R package version 0.6.2. Available from http://CRAN.R-project.org/package=stringr.
46. Willing E-M, Hoffmann M, Klein JD, Weigel D, Dreyer C (2011) Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics, 27, 2187-2193.
47. Xu J, Turner A, Little J, Bleecker ER, Meyers DA (2002) Positive results in association studies are associated with departure from Hardy-Weinberg equilibrium: hint for genotyping error? Human Genetics, 111, 573-574.
48. Zamudio S (2009) Notas sobre el género Berberis (Berberidaceae) en México. Acta Botánica Mexicana, 87, 31-70.
49. Zhang H, Hare MP (2012) Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters. Heredity, 108, 616-625.