Using reference genome of the species itself is optimal for SNP calling, finds study

With the advent of next-generation sequencing technologies, restriction-site associated DNA sequencing (RAD-seq) has become a mainstream method for rapidly obtaining high-density single nucleotide polymorphisms (SNPs) in organisms due to its independence from reference genomes. However, few studies have examined the impact of using closely related species as reference genomes versus using the species itself as a reference genome.