Tables and Figures
Figure 1. The assembled B. l. tsinlingensis genome and
its codon usage characteristics. A: Heatmap of chromosome interactions
in B. l. tsinlingensis . B: Circos graph of the genome
characteristics. Shown from the outer circle to the inner ring are the
gene distribution, tandem repeats (TRP), long tandem repeats (LTRs),
short interspersed nuclear elements (SINEs), long interspersed nuclear
elements (LINEs), DNA elements (DNA), and genome GC content. C:Codon usage bias. Values of the codon bias index (CBI) on the frequency
of guanine + cytosine at the synonymous third position of codons (GC3s)
were determined using the nucleotide sequences of all predicted genes
concatenated for individual species. D: The third position of
the synonymous codon of these species.
Figure 2. Whole genome duplication events and the expanding
genome. A: Ss4R event in B. l. tsinlingensis and other species.
Solid lines are values for the 4DTv of paralogous genes in these 11
species; dotted lines are 4DTv of orthologs between B. l.
tsinlingensis and other species. B: The genome composition of
these species, including coding exons, tandem repeats, DNA elements,
LINEs, SINEs, LTR elements, and others. C: The TE insertion
times of these species.
Figure 3. Hox clusters in these species. Both Ts3R event
and Ss4R event are shown in this figure.
Figure 4. Comparative genomics of B. l. tsinlingensis and
other closely related species. A: Statistics of all
orthologous/paralogous gene numbers in these species. B: A Venn
diagram displaying the overlap in orthologous genes in salmonids and all
3 other fishes. C: The phylogenetic relationship and divergence
time in these species. L. oculatus was used as an outgroup
species. The red dot indicates that fossil record evidence was used here
to adjust our divergence time results. D: The relative
evolutionary rate of these species; the reference species was B.
l. tsinlingensis . E: The Ka/Ks distribution of these species
calculated by PAML.