Chromosome-Level Genome Assembly of (Teleostei, Cyprinidae) and Population Genomics of the Complex: Impacts of Geological and Climate Changes on Species Evolution in Southwest China.

The genus is distributed in the eastern three rivers on the Yunnan-Guizhou Plateau and its adjacent regions, located to the southeast of the Qinghai-Tibet Plateau. Its origin and evolution are likely influenced by the uplift of the Qinghai-Tibet Plateau. However, the historical impact of geological events on the divergence and distribution of this fish group has not been fully elucidated. In this study, we successfully assembled a chromosome-level genome for , which is approximately 1.21 Gb in length with a contig N50 of 8.63 Mb. The completeness of the genome assembly was assessed with a BUSCO score of 94.78%. A total of 30,597 protein-coding genes were predicted, with 93.92% functionally annotated. Phylogenetic analysis indicated that was closely related to , and the divergence of the subfamily Labeoninae coincided with the significant uplift events of the Qinghai-Tibet Plateau. Additionally, we analyzed 75 samples of and from five populations, yielding 1.82 Tb of clean data and identifying 891,303,336 high-quality SNP sites. Population structure analyses indicated that the populations were clustered into five distinct groups, demonstrating significant genetic differentiation among them and the presence of cryptic species within this genus. Analyses of linkage disequilibrium decay and selective sweep indicated that the Pearl River population exhibited relatively higher genetic diversity compared with the populations from other drainages, and none of the populations showed evidence of expansion. Notably, the two population declines coincided with the early Pleistocene and Quaternary glaciation. It can be assumed that the geological movements of the Qinghai-Tibet Plateau and the Quaternary glaciation contributed to the decline in populations and shaped their current size. The population genomics results showed that the present distribution pattern of was the outcome of a series of geological events following the uplift of the Qinghai-Tibet Plateau. This study reconstructed the geological evolutionary history of the region from the perspective of species evolution. Furthermore, our study presents the first genome-wide analysis of the genetic divergence of .