2013
DOI: 10.7717/peerj.203
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ezRAD: a simplified method for genomic genotyping in non-model organisms

Abstract: Here, we introduce ezRAD, a novel strategy for restriction site–associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencin… Show more

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Cited by 210 publications
(200 citation statements)
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“…The reduced genome representation can be achieved in several ways: (1) by using various steps for reducing genome complexity such as RAD (restriction-site associated DNA) sequencing and related approaches (Miller et al, 2007;Baird et al, 2008;Peterson et al, 2012;Toonen et al, 2013); (2) by targeting only the expressed parts of the genome (i.e., RNAseq, Wang et al, 2009);or (3) by isolating specific known regions of the genome through hybridization-based sequence capture or targeted amplification (Good, 2011;Grover et al, 2012), although the latter approach requires a pre-existing reference sequence from the target species or a close relative. Alternative approaches combine transcriptome and genome sequence data (e.g., Lamichaney et al,.…”
Section: Next-generation Population Genomicsmentioning
confidence: 99%
“…The reduced genome representation can be achieved in several ways: (1) by using various steps for reducing genome complexity such as RAD (restriction-site associated DNA) sequencing and related approaches (Miller et al, 2007;Baird et al, 2008;Peterson et al, 2012;Toonen et al, 2013); (2) by targeting only the expressed parts of the genome (i.e., RNAseq, Wang et al, 2009);or (3) by isolating specific known regions of the genome through hybridization-based sequence capture or targeted amplification (Good, 2011;Grover et al, 2012), although the latter approach requires a pre-existing reference sequence from the target species or a close relative. Alternative approaches combine transcriptome and genome sequence data (e.g., Lamichaney et al,.…”
Section: Next-generation Population Genomicsmentioning
confidence: 99%
“…Profi ling a large number of single nucleotide polymorphisms (SNPs) was only realistically possible for organisms with well-developmed genomic resources, and the high cost of developing these resources has been a major impediment to studies for non-model organisms, e.g. deer [16]. However, most of the current studies assessing phylogeny or population genetics of wild animals require only a reduced set of SNPs that are spread across the genome [7,17,18].…”
Section: Introductionmentioning
confidence: 99%
“…KU572435), assembled using next-generation sequencing. Small fragments of P. lobata samples were collected from Oahu, Hawaii (China Walls, Toonen et al (2013). Individually barcoded samples were pooled, quality-checked and sequenced on an Illumina MiSeq V R Analyzer at the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology [HIMB], Kaneohe, HI).…”
mentioning
confidence: 99%