Reference genomes from distantly related species can be used for discovery of single nucleotide polymorphisms to inform conservation management (2019)
Type of ContentJournal Article
AuthorsGalla SJ, Forsdick NJ, Brown L, Hoeppner MP, Knapp M, Maloney RF, Moraga R, Santure AW, Steeves TEshow all
© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-quality reference genomes for single nucleotide polymorphism (SNP) discovery using the critically endangered kakī/black stilt (Himantopus novaezelandiae) and four Charadriiform reference genomes as proof of concept. We compare diversity estimates (i.e., nucleotide diversity, individual heterozygosity, and relatedness) based on kakī SNPs discovered from genotyping-by-sequencing and whole genome resequencing reads mapped to conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric (pied stilt, Himantopus himantopus) and conspecific reference genomes. Results indicate that diversity estimates calculated from SNPs discovered using closely related reference genomes correlate significantly with estimates calculated from SNPs discovered using a conspecific genome. Congeneric and confamilial references provide higher correlations and more similar measures of nucleotide diversity, individual heterozygosity, and relatedness. While conspecific genomes may be necessary to address other questions in conservation, SNP discovery using high-quality reference genomes of closely related species is a cost-effective approach for estimating diversity measures in threatened species.
CitationGalla SJ, Forsdick NJ, Brown L, Hoeppner MP, Knapp M, Maloney RF, Moraga R, Santure AW, Steeves TE (2019). Reference genomes from distantly related species can be used for discovery of single nucleotide polymorphisms to inform conservation management. Genes. 10(1). 9-9.
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Keywordsconservation genomics; conservation genomics gap; SNP discovery; B10K; threatened species; birds
ANZSRC Fields of Research41 - Environmental sciences::4104 - Environmental management::410401 - Conservation and biodiversity
31 - Biological sciences::3105 - Genetics::310509 - Genomics