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

Autor: Bredemeyer KR; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA., Hillier L; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Harris AJ; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA., Hughes GM; School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland., Foley NM; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA., Lawless C; School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland., Carroll RA; Department of Animal Sciences, University of Missouri, Columbia, MO, USA., Storer JM; Institute for Systems Biology, Seattle, WA, USA., Batzer MA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA., Rice ES; Department of Animal Sciences, University of Missouri, Columbia, MO, USA., Davis BW; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA., Raudsepp T; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA., O'Brien SJ; Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL, USA., Lyons LA; Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA., Warren WC; Department of Animal Sciences, University of Missouri, Columbia, MO, USA. warrenwc@missouri.edu., Murphy WJ; Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA. wmurphy@cvm.tamu.edu.; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA. wmurphy@cvm.tamu.edu.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2023 Nov; Vol. 55 (11), pp. 1953-1963. Date of Electronic Publication: 2023 Nov 02.
DOI: 10.1038/s41588-023-01548-y
Abstrakt: 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.
(© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
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