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.