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Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution.

ABSTRACT: The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.

SUBMITTER: Bredemeyer KR

PROVIDER: S-EPMC10845050 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution.

Bredemeyer Kevin R KR Hillier LaDeana L Harris Andrew J AJ Hughes Graham M GM Foley Nicole M NM Lawless Colleen C Carroll Rachel A RA Storer Jessica M JM Batzer Mark A MA Rice Edward S ES Davis Brian W BW Raudsepp Terje T O'Brien Stephen J SJ Lyons Leslie A LA Warren Wesley C WC Murphy William J WJ

Nature genetics 20231102 11

The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes ...[more]

PMID: 37919451

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Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution.

Publications

Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution.

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