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Article
Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches
PLoSONE (2014)
  • Karen E. Mock, Utah State University
Abstract
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species...
Disciplines
Publication Date
2014
DOI
https://doi.org/10.1371/journal.pone.0095292.t001
Publisher Statement
USDA Forest Service Publication
Citation Information
Karen E. Mock. "Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches" PLoSONE Vol. 9 Iss. 4 (2014) p. e95292
Available at: http://works.bepress.com/karen_mock/86/