Chromosome‐Level Genome Assembly of Otocolobus manul Provides Insights Into High‐Altitude Adaptation and Evolutionary Traits

ABSTRACT The Otocolobus manul , a small felid endemic to the high‐altitude Qinghai‐Tibet Plateau, lacks a high‐quality chromosome‐level genome, hindering study of its evolutionary adaptations. This study aimed to construct such a genome and investigate its genetic basis for high‐altitude adaptation. We generated a de novo chromosome‐scale assembly using an integrated approach of PacBio HiFi long‐reads, Illumina short‐reads, and Hi‐C scaffolding. The resulting 2.55 Gb genome was anchored to 19 chromosomes (contig N50 = 96.32 Mb) and contained 22,699 protein‐coding genes. Comparative genomic analysis across felids revealed 13 expanded gene families in O. manul , functionally enriched in processes like glycolysis/gluconeogenesis and the HIF1 signalling pathway. Phylogenetic analysis placed O. manul as sister to Prionailurus , with an estimated divergence time of 6.10–7.04 million years ago, and identified positive selection signals linked to adaptation. Furthermore, we found that the nuclear genome supports a sister relationship between O. manul and Prionailurus (they are closely related species), while the mitochondrial genome suggests a closer relationship with Felis . This significant mito‐nuclear phylogenetic discordance is primarily attributed to incomplete lineage sorting (ILS). This de novo chromosome‐level genome assembly of O. manul provides a crucial resource for evolutionary and conservation studies. The findings specifically highlight significant genetic enrichments in hypoxia‐responsive pathways, suggesting its molecular adaptation to the extreme plateau environment.