Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management.

摘要: Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance recovery. However, a lack of readily available resources, including conspecific reference genomes, often limits the inclusion data. Here, we investigate utility closely related high-quality genomes for single nucleotide polymorphism (SNP) discovery using critically endangered kakī/black stilt (Himantopus novaezelandiae) and four Charadriiform as proof concept. We compare diversity estimates (i.e., diversity, individual heterozygosity, relatedness) based on kakī SNPs discovered genotyping-by-sequencing whole genome resequencing reads mapped conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric stilt, Himantopus himantopus) genomes. Results indicate that calculated correlate significantly with genome. Congeneric references provide higher correlations more similar measures relatedness. While may be necessary address other questions in conservation, SNP is cost-effective approach estimating threatened species.