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.