Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Claire M Wade,Bianca Haase,Hamutal Mazrier,Catherine E Grueber,Georgina Samaha

doi:10.1186/s12864-021-07899-2

Abstract

BackgroundWhile recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus).ResultsAlignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases.ConclusionsThe high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes.

Highlights

While recent advances in genomics has enabled vast improvements in the quantification of genomewide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits
Cross-species whole genome sequence (WGS) alignment and variant calling using the Felis_catus_ 9.0 (felCat9) reference assembly Genomic DNA of four Sumatran tigers, four cheetahs and four snow leopards was pooled by species in equimolar ratios and sequenced
Whole genome sequences for seven Sumatran tigers, six cheetahs and one snow leopard were downloaded from sequence read archive (SRA) [42]

Summary

Introduction

While recent advances in genomics has enabled vast improvements in the quantification of genomewide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. Allelic variation is essential to preserving species’ genetic integrity and maintaining functioning ecosystems, as genetically diverse populations tend to have higher fitness and adaptive capacity [3] Given their conservation status, many big cats are the subjects of Species Survival Plans (SSP) [4, 5]; internationally coordinated programmes that manage ex situ breeding and aim for healthy, self-sustaining and genetically diverse populations. ‘non-model species’ refers to those with limited genomic resources, reference genomes

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Conclusion