Salmonid-specific fourth vertebrate WGD
The last WGD for most teleosts occurred approximately 320 Mya (Jaillon et al. 2004; Kasahara et al. 2007); because of its basal occurrence in the teleost radiation, little is known about this WGD event. However, the salmonid-specific fourth vertebrate WGD (Ss4R) took place in the common ancestor of salmonids approximately 80 Mya (Macqueen& Johnston 2014; Near et al. 2012), which is the most recent WGD event in vertebrates. In addition, B. l. tsinlingensis is the most ancient species among known salmonids and thus particularly valuable for the study of salmonid evolution. To elucidate the history of Ss4R, we screened the paralogs of all species by McScan (Tang et al. 2008) and calculated the distribution of the rate of transversions on fourfold degenerate synonymous sites (4DTv). The peaks of all salmonids were concentrated near values of 4DTv at 0.2–0.3, which is the Ss4R event that occurred ~80 Mya in all salmonids (Macqueen & Johnston 2014; Near et al. 2012). We also screened the orthologs with syntenic blocks between B. l. tsinlingensis and all other species separately. Furthermore, we calculated the 4DTv of the homologs in the other species, which showed that peaks of the 4DTv of the salmonids were around 0.7–0.9 (Figure 2A ). Taken together, Ss4R occurred before the divergence of salmonids from Esociformes, and all salmonids shared the Ss4R event.
Because of the Ss4R event, the genome size of all salmonids (which ranges from 1.85 Gb to 2.97 Gb) is much larger than that of other related species (which ranges from 1.19 Gb to 1.68 Gb). The TEs in salmonids are much more abundant compared with other species, especially the tandem repeats, DNA elements, and LINE elements (Figure 2B ). These three types of TEs may play important roles in WGD and contribute to the larger genome size of salmonids. In addition, the peaks of the TEs insertion time of salmonids were all around 40–80 Mya, which is earlier than Ss4R (Figure 2C ). This indicates that the WGD and TE insertion events occurred in the common ancestor of salmonid fishes.