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

Details

Serval ID
serval:BIB_005801125839
Type
Article: article from journal or magazin.
Collection
Publications
Title
Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.
Journal
Molecular Ecology Resources
Author(s)
Mastretta-Yanes A., Arrigo N., Alvarez N., Jorgensen T.H., Piñero D., Emerson B.C.
ISSN
1755-0998 (Electronic)
ISSN-L
1755-098X
Publication state
Published
Issued date
2015
Peer-reviewed
Oui
Volume
15
Number
1
Pages
28-41
Language
english
Abstract
Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.
Keywords
de novo assembly, error rate, optimization, RAD sequencing, replicates, Stacks
Pubmed
Web of science
Create date
22/09/2014 10:50
Last modification date
20/08/2019 13:22
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