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

Stephanie J Galla,Richard F Maloney,Anna W Santure,Michael Knapp,Tammy E Steeves,Natalie J Forsdick,Marc Hoeppner,Roger Moraga,Liz Brown

doi:10.3390/genes10010009

Stephanie J Galla, Richard F Maloney + Show 7 more

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https://doi.org/10.3390/genes10010009

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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.

Highlights

IntroductionThe field of conservation genetics is in transition from using relatively few genetic markers (e.g., microsatellites, mitochondrial sequences) to using thousands of genome-wide single nucleotide polymorphisms (SNPs) discovered with high-throughput sequencing technologies (HTS) to inform conservation management of threatened species
The field of conservation genetics is in transition from using relatively few genetic markers to using thousands of genome-wide single nucleotide polymorphisms (SNPs) discovered with high-throughput sequencing technologies (HTS) to inform conservation management of threatened species
While the promise of a conservation genomic approach has been heralded for well over a decade [5], the uptake of these technologies by conservation management has been slow [6,7]. This time lag between technology availability and implementation may be caused by several interconnected issues, including a disconnect between conservation genetic researchers and practitioners [8,9], the time it takes for geneticists to upskill in bioinformatic expertise [6,7,10], and initial expense for HTS sequence production and generation of genomic resources

Summary

Introduction

The field of conservation genetics is in transition from using relatively few genetic markers (e.g., microsatellites, mitochondrial sequences) to using thousands of genome-wide single nucleotide polymorphisms (SNPs) discovered with high-throughput sequencing technologies (HTS) to inform conservation management of threatened species. While the promise of a conservation genomic approach has been heralded for well over a decade [5], the uptake of these technologies by conservation management has been slow [6,7] This time lag between technology availability and implementation ( termed the ‘conservation genomics gap’ [7]) may be caused by several interconnected issues, including a disconnect between conservation genetic researchers and practitioners [8,9], the time it takes for geneticists to upskill in bioinformatic expertise [6,7,10], and initial expense for HTS sequence production and generation of genomic resources (e.g., a high-quality reference genome). While reference genomes are preferred for conservation genomic research, they are often unavailable for threatened species or out of reach for resource-constrained conservation projects (e.g., [18])

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