Discussion
B. l. tsinlingensis belongs to Brachymystax , which is the most ancient species of salmonid fish. Its genomic resources not only provide new insights into its evolution but also supply basic data for future studies of salmonid evolution. We presented the first chromosome-level genome assembly of B. l. tsinlingensis with an N50 ~50.15 Mb. Several different methods confirmed the high quality and accuracy of the assembled genome. Comparison of the genome of B. l. tsinlingensis with that of other salmonids revealed that the basic genome characters of salmonids were similar after the Ss4R event. Ss4R also caused an increase in TEs in salmonids and the number of genes, and several positively selected genes were specific to salmonids. The evolutionary rate of all salmonids was slower compared with other species. In addition, there is a pressing need to protect these endangered species. Habitat conservation for B. l. tsinlingensis is particularly important for ensuring the long-term survival and viability of B. l. tsinlingensis populations.