Introduction
Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages; it is widely accepted that three rounds of WGD have occurred during vertebrate evolution: 1R and 2R are shared by the jawed vertebrates, and the third teleost-specific WGD (Ts3R) occurred at basally in the teleost radiation ~320 million years ago (Mya) (Jaillon et al. 2004; Kasahara et al. 2007). However, the fourth salmonid-specific WGD (Ss4R) occurred in the common ancestor of salmonids ~80 Mya after their divergence from Esociformes ~125 Mya (Macqueen & Johnston 2014; Near et al. 2012). WGD events help species expand their genome size and evolve new characters; thus, studying the evolutionary fate of duplicated genomes, especially recently duplicated genomes, can provide valuable evolutionary insights.
Brachymystax lenoktsinlingensisis an endangered freshwater fish that is endemic to the middle part of the Qinling Mountains, especially the Heihe, Shitouhe, Xushui, and Taibaihe Rivers (Froese & Pauly 2014). Study of B. l. tsinlingensis could greatly aid our understanding of salmonid evolution given that it is the outgroup species of all known salmonids. However, only mitochondrial genome data have been published (Si et al. 2012; Yu & Kwak 2015); genome and transcriptome data of B. l. tsinlingensis are still lacking by comparison. In this study, we conducted the first chromosome-level genome assembly of B. l. tsinlingensis by combining Nanopore long reads, Hi-C data, and Illumina short reads. Comparative genomics analysis with other related species revealed that the salmonids have a unique GC content and codon usage, have undergone a common WGD event and a burst of transposon-mediated repeat expansion, have a slower evolution rate, and possess specific expanded genes and unique positively selected genes. Overall, these findings provide new insight into the evolutionary history of salmonids and will aid future studies of salmonid evolution.