Genome evolution in a Tibetan highland catfish reveals chemosensory gene reduction and recent sex chromosome emergence

Abstract Catfishes (order Siluriformes) inhabit diverse aquatic environments worldwide, ranging from tropical lowlands to fast‐flowing mountain rivers. However, the contribution of genomic variation to ecological diversification in catfishes, particularly within high‐altitude lineages, remains poorly understood. Here, we investigated genome evolution in an extreme environment by focusing on Glyptosternum maculatum , the highest‐altitude‐dwelling catfish known and a basal lineage of Glyptosternoid fishes. We generated a high‐quality, haplotype‐resolved genome assembly using PacBio HiFi and Hi‐C sequencing. The two phased haplotypes span 741.8 Mb and 753.7 Mb, with contig N50 values >4 Mb, representing a substantial improvement in continuity and accuracy over previous assemblies. Comparative genomic analyses revealed significant contraction of gene families associated with G protein‐coupled receptor activity, particularly olfactory receptor (OR) and trace amine‐associated receptor (TAAR) genes. Water‐soluble OR subfamilies showed a pronounced reduction relative to other catfishes, suggesting lineage‐specific remodeling of chemosensory repertoires that may reflect ecological specialization in high‐altitude river systems. Population genetic analyses identified chromosome 11 as the sex chromosome, harboring an ~0.97 Mb sex‐determining region (SDR) consistent with an XX/XY system. The X and Y chromosomes are highly similar and lack evolutionary strata, indicating a young, homomorphic pair. Despite limited sequence divergence, the SDR shows an enrichment of LINE retrotransposons, with evidence of recent transposable element accumulation extending into adjacent regions. Our results provide a chromosome‐level genomic resource for Glyptosternoid fishes and offer new insights into sensory gene evolution and the early dynamics of sex chromosome differentiation in a high‐altitude teleost.