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.