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Four new genome sequences of the Pallas's cat (Otocolobus manul): an insight into the patterns of within-species variability

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Jul 25, 2024 version files 1.92 GB
Sep 19, 2024 version files 1.93 GB
Oct 16, 2024 version files 1.93 GB

Abstract

Manul (Otocolobus manul) is the only representative of the genus Otocolobus belonging to the Leopard Cat lineage. Their habitat is characterized by harsh environmental conditions. Although their populations are probably more stable than previously thought, it is still the case that their population size is declining. The main cause of their decline is the destruction of their natural habitat, which together with their natural behavior results in geographically fragmented populations and a potential threat of loss of genetic variability. Conservation programs exist to protect manuls, but those based on captive breeding are often unsuccessful due to their increased susceptibility to diseases. The manul is therefore a suitable model species for evolutionary and diversity studies as well as for studying mechanisms of adaptation to harsh environment and mechanisms of susceptibility to diseases. Whole genome sequencing (WGS) is an important tool for such studies, providing base-by-base view of the genome. Recently, the genome of the Otocolobus manul based on nanopore long-range sequencing has been published. Using whole genome resequencing via the Illumina platform, we obtained information on the genomes of four other manuls aiming to better understand inter-and intraspecific variation of the species. The parameters characterizing the quality of sequencing were within the standard range, all four genomes analyzed were similar in most characteristics. On average, we detected a total of 3,668,327 polymorphic variants. Information on different types of structural varinats not available from the reference genome was retrieved. The average whole-genome heterozygosity detected was almost identical to that found in the Otocolobus manul reference genome. In this context, we performed a more detailed analysis of the candidate gene EPAS1 potentially related to adaptation to the hypoxic environment. This analysis revealed both inter-and intraspecific variation, confirmed the presence of a previously described non-synonymous substitution in exon 15 unique to manuls and identified three additional unique non-synonymous substitutions located in so far not analyzed EPAS1 exonic sequences.