ezRAD: a simplified method for genomic genotyping in non-model organisms

PeerJ. 2013 Nov 19;1:e203. doi: 10.7717/peerj.203. eCollection 2013.

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 sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes) that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.

Keywords: Genotype-by-sequencing; NGS; Next-generation sequencing; RAD tag; RAD-seq; RADseq; Restriction site associated DNA (RAD).

Grant support

This work was funded in part by the National Science Foundation (Grant OCE-1260169), and the National Oceanic and Atmospheric Administration (NMSP MOA#2005-008/66882). Additional support for the co-authors came from the National SeaGrant Program, the Hawaiʻi Coral Reef Initiative, the Seaver Institute, Fulbright – Spanish Ministry of Science and Technology, and the Japanese Society for the Promotion of Science. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.