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

ABSTRACT:

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 Carya, isolating sites where genetic variation was restricted to a single Carya species (i.e., species-informative SNPs). We leveraged these SNPs to identify both full-species and hybrid Carya specime

SUBMITTER: Literman RA 

PROVIDER: S-EPMC8861591 | biostudies-literature | 2022 Jan-Feb

REPOSITORIES: biostudies-literature