Chromosome-level genome assembly for Sichuan taimen (hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage

Abstract

The Chuanshan hucho (Hucho bleekeri) is one of the largest freshwater salmonids, and located at the base of the Salmoninae phylogeny. Facing a serious risk of extinction, the Chuanshan hucho has attracted widespread concern and has been listed as national first-level protected animal in China. Currently, biological research and conservation policies of the Chuanshan hucho are in full progress, but the complete genome sequence is still unknown which hindered the advance of its conservation genomics. In this study, we provided the first chromosome-level genome for Chuanshan hucho, the final genome size was ∼3.45 Gb with 44 chromosomes. The hucho genome contained 44.15% tandem repetitive sequence, which exceeded all sequenced salmonid fishes. According to the nuclear sequence, the divergence time ofHuchoandBrachymystaxwas estimated as 12.29 Mya, and the effective population size of Chuanshan hucho declined from 1 Mya. The genomic resource in this article will promote the protection of Chuanshan hucho and evolutionary genetics studies of salmonids.