Genome annotation
From the assembled genome, the repeat sequences were identified in the
genome of B. l. tsinlingensis . Repeat sequences accounted for
64.48% of the genome, and the DNA transposons (20.78%) were the most
abundant repeat type (Table S12-S13 ). For genome annotation, a
total of 55,706 genes were predicted using different annotation methods,
and the gene structure was similar to other published genomes of related
species (Figure S10 ). The functional annotation results
revealed that among these 55,706 protein-coding genes, homologous genes
could be found in public databases for 90.14% (50,214) of the genes,
which indicated that the gene structure annotation was robust
(Table S14 ). The gene density, all types of repeat sequences,
and GC density of the assembly are shown in Figure 1B . Owing to
the Ss4R event, codon usage in salmonids was uniform (Figure
1C ). In addition, the third position of the synonymous codon of
salmonids was more likely to be G or C, which differs from other fishes
(Figure 1D ).