Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution
Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution
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DOI：
10.1038/s41588-023-01548-y
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发表时间：
2023-11-02
期刊：
影响因子：
30.8
通讯作者：
Murphy, William J.
中科院分区：
文献类型：
--
作者：
Bredemeyer, Kevin R.;Hillier, LaDeana;Murphy, William J.
由于二倍体基因组组装固有的挑战，人们对结构动态基因组区域在物种形成中的作用知之甚少。在这里，我们通过对三个种间 F1 杂交体的基因组进行定相以生成近乎无间隙的单倍型组装体，重建了五种猫科动物结构变异的进化动力学。我们发现，与类人猿相比，猫的基因组缺乏片段重复，这解释了它们显着的核型稳定性。 X染色体是结构变异的热点，包括在具有超基因特征的大型重组沙漠中通过倒位富集。 X连锁大卫星DXZ4的进化速度比99.5%的基因组都要快，阐明了它在猫科动物杂交不相容性中的作用。解析的感觉基因库揭示了与生态形态适应、社会性和驯化相关的功能拷贝数变化。这项研究强调了无间隙基因组在揭示核型进化、生殖隔离和生态位适应的结构机制方面的价值。
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.