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

Area of Science:

• Comparative genomics
• Evolutionary biology
• Speciation research

Background:

• Understanding the role of genomic structural variation in speciation is limited by challenges in diploid genome assembly.
• Previous studies lacked high-resolution genomic data to explore structural evolution across closely related species.

Purpose of the Study:

• To reconstruct the evolutionary dynamics of structural variation in five cat species.
• To identify genomic mechanisms underlying karyotypic stability, reproductive isolation, and adaptation in felids.

Main Methods:

• Generated near-gapless single-haplotype assemblies by phasing genomes of three interspecies F1 hybrids.
• Analyzed structural variations, including segmental duplications and inversions, across cat genomes.
• Investigated the evolution of the X chromosome and specific genes like DXZ4.

Main Results:

• Cat genomes exhibit fewer segmental duplications than great apes, correlating with high karyotypic stability.
• The X chromosome is a hotspot for structural variation, featuring inversions within a recombination desert potentially acting as a supergene.
• Rapid evolution of the X-linked macrosatellite DXZ4 contributes to felid hybrid incompatibility.
• Functional copy number changes in sensory genes are linked to ecomorphological adaptations, social behavior, and domestication.

Conclusions:

• Near-gapless genome assemblies are crucial for revealing structural mechanisms of karyotypic evolution.
• Structural variations, especially on the X chromosome, are key drivers of reproductive isolation and adaptation in cat species.
• This study provides a foundation for understanding the genetic basis of feline speciation and adaptation.