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

Abstract

Background While 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). Results Alignment 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. Conclusions The 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.

Genetic diversity in global populations of the critically endangered addax (Addax nasomaculatus) and its implications for conservation

“…Reads were aligned using BWA (Li & Durbin, 2009) to the reference genome of the closely related scimitar‐horned oryx ( Oryx dammah assembly version 1.1, GCF_014754425.2; Humble et al, 2020). Preliminary analyses demonstrated highly concordant results using de novo SNP calling with Stacks (using m = 6, M = 2, n = 2 after parameterization), which is in line with other studies, suggesting that genomes of closely related species are suitable for SNP discovery in a conservation context (Galla et al, 2019; Samaha et al, 2021). SNPs were called using Stacks within a custom Snakemake pipeline (Köster & Rahmann, 2012).…”

The influence of gene flow on population viability in an isolated urban caracal population

“…First, caracals are not domestic cats, and thus the validity of using parameters from the domestic cat genome remains uncertain. However, felid genomes appear to be highly conserved (Armstrong et al., 2022; Samaha et al., 2021), suggesting that such parameters may not greatly vary across felids. Second, in our baseline model, we assume that only nonsynonymous mutations impact fitness, whereas our sensitivity analysis suggests that noncoding deleterious variation may also play an important role (Figure 6).…”

“…We used BWA-MEM (Li, 2013) to align paired-end 150 bp raw sequence reads to the domestic cat genome (felCat9.0; Buckley et al, 2020), followed by removal of low-quality reads and PCR duplicates. In the absence of a caracal reference genome, we opted to use this high-quality reference genome given the high degree of synteny that is observed in felids (Armstrong et al, 2022;Samaha et al, 2021). As we do not have a database of known variants, we did not carry out Base Quality Score Recalibration but instead carried out hard filtering of genotypes (see below).…”

Gene pseudogenization in fertility-associated genes in cheetah (Acinonyx jubatus), a species with long-term low effective population size

“…In addition to ARL13A, CFAP119 (Cilia and Flagella Associated Protein 119, also known as Coiled-Coil Domain-Containing Protein 189 (CCDC189)) is also potentially involved in male fertility. Many CCDC genes have previously been linked to male fertility in mice and humans (Tang et al, 2017;Zhang et al, 2019), and a deleterious mutation in CCDC39 has previously been identified in the cheetah (Samaha et al, 2021).…”

“…Although many studies have considered the impacts of functionally-damaging missense variants in species with low N e (Daetwyler et al ., 2014; Dobrynin et al ., 2015; Marsden et al ., 2016; Samaha et al ., 2021), elevated rate of allele loss (Masel, 2011) , and increased likelihood of homozygous expression of a recessive deleterious allele (Mukai et al ., 1972; Charlesworth and Charlesworth, 1987; Charlesworth and Willis, 2009; Bosse et al ., 2019), pseudogenization as a result of population decline has often been overlooked in the literature.…”