Reference-free discovery of nuclear SNPs permits accurate, sensitive identification of (hickory) species and hybrids.

PREMISE

DNA-based species identification is critical when morphological identification is restricted, but DNA-based identification pipelines typically rely on the ability to compare homologous sequence data across species. Because many clades lack robust genomic resources, we present here a bioinformatics pipeline capable of generating genome-wide single-nucleotide polymorphism (SNP) data while circumventing the need for any reference genome or annotation data.

METHODS

Using the SISRS bioinformatics pipeline, we generated de novo ortholog data for the genus , isolating sites where genetic variation was restricted to a single species (i.e., species-informative SNPs). We leveraged these SNPs to identify both full-species and hybrid specimens, even at very low sequencing depths.

RESULTS

We identified between 46,000 and 476,000 species-identifying SNPs for each of eight diploid species, and all species identifications were concordant with the species of record. For all putative F hybrid specimens, both parental species were correctly identified in all cases, and more punctate patterns of introgression were detectable in more cryptic crosses.

DISCUSSION

Bioinformatics pipelines that use only short-read sequencing data provide vital new tools enabling rapid expansion of DNA identification assays for model and non-model clades alike.