Near telomere-to-telomere genome reveals the phylogenomics and hibernation-related evolution in Tibetan brown bear (Ursus arctos pruinosus)

Abstract

The Tibetan brown bear ( Ursus arctos pruinosus ) is an apex predator endemic to the Qinghai-Xizang Plateau (QXP) with crucial ecological status, while high-quality genomic resources for studying its adaptation to the plateau environment remain scarce. Here, we generated a near-T2T chromosome-level genome assembly of a female Tibetan brown bear from QXP, using PacBio HiFi and Hi-C sequencing. The final assembly spans 2.42 Gb, with scaffold N50 of 72.35 Mb, contig N50 of 66.56 Mb and GC content of 42.36%. Comparative genomic analyses revealed high chromosomal synteny between Tibetan brown bear and polar bear. Demographic reconstruction of Tibetan brown bear demonstrated a population expansion during the early Pleistocene, followed by two significant population bottlenecks at approximately 2 Mya (pre-Poyang Glaciation) and 0.1 Mya (the Last Glacial Period), leading to a cumulative effective population size reduction of nearly 80%. Notably, analyses of candidate hibernation-related pathways in the Tibetan brown bear revealed that it exhibits distinct carbohydrate-dominated metabolic signatures compared to the lipid metabolism-dependent hibernation pattern of the North American brown bear. This distinct metabolic adaptation highlights its unique adaptive mechanisms for surviving extreme QXP environments. This high-quality genome assembly provides a valuable genomic resource for exploring the evolutionary history of Ursidae and facilitates future conservation and management. In this study, we presented a near telomere-to-telomere genome of a female Tibetan brown bear from Qinghai, China. The final assembly spans 2.42 Gb, with scaffold N50 of 72.35 Mb, contig N50 of 66.56 Mb and GC content of 42.36%. Demographic reconstruction of Tibetan brown bear demonstrated an population expansion during the early Pleistocene, followed by two significant population bottlenecks at approximately 2 Mya (pre-Poyang Glaciation) and 0.1 Mya (the Last Glacial Period), leading to a cumulative effective population size reduction of nearly 80%. Tibetan brown bear candidate hibernation-related pathway analyses revealed a specific carbohydrate-dominated metabolic strategy that differs strikingly from the lipid metabolism-dependent hibernation pattern of North American brown bear.