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

1
School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
2
Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
3
Te Manahuna, Department of Conservation, Twizel 7901, New Zealand
4
Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
5
Science and Policy Group, Department of Conservation, Christchurch 8011, New Zealand
6
Tea Break Bioinformatics Ltd., Palmerston North 4144, New Zealand
7
School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
*
Authors to whom correspondence should be addressed.
Received: 8 November 2018 / Revised: 16 December 2018 / Accepted: 19 December 2018 / Published: 22 December 2018
(This article belongs to the Special Issue Conservation Genetics and Genomics)
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Abstract

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. View Full-Text
Keywords: conservation genomics; conservation genomics gap; SNP discovery; B10K; threatened species; birds conservation genomics; conservation genomics gap; SNP discovery; B10K; threatened species; birds
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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MDPI and ACS Style

Galla, S.J.; Forsdick, N.J.; Brown, L.; Hoeppner, M.P.; Knapp, M.; Maloney, R.F.; Moraga, R.; Santure, A.W.; Steeves, T.E. Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management. Genes 2019, 10, 9.

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