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

TLDR

The authors present ezRAD, a simplified RAD sequencing strategy that requires minimal technical expertise and equipment, and apply it to diverse non‑model organisms to demonstrate its utility and flexibility. ezRAD employs standard Illumina TruSeq library kits and accepts any restriction enzyme, allowing laboratories to outsource library preparation and sequencing with virtually no additional investment. ezRAD opens RAD‑seq to any lab capable of DNA extraction and restriction digest, enabling SNP discovery and targeted amplicon sequencing in understudied 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 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.