Comparative analysis with other species
Using the annotated genomes, we constructed orthologous gene clusters ofB. l. tsinlingensis, with other salmonid fishes and other
outgroup fishes. There were 31,296 gene families identified in these 11
species, and B. l. tsinlingensis contained 19,145 gene families.
Because salmonid fishes have almost twice the number of genes compared
with other species, the number of gene families is also twice that of
other species (Figure 4A ). In these 31,296 gene families,
11,343 gene families were salmonid-specific. Salmonids shared 16,840
(53.81%) gene families with Esox lucius , 14,783 (47.24%) withDanio rerio , and 13,491 (43.11%) with Lepisosteus
oculatus (Figure 4B ). A total of 1,216 1:1 single-copy
orthologous genes were identified and used to construct phylogenetic
trees, including a 4DTv tree, CDS tree, and protein tree. All of these
trees recovered the same phylogenetic topology with high confidence
(Figure S11-S13 ). B. l. tsinlingensis and 8 other
salmonid fishes formed a Salmonidae cluster, and B. l.
tsinlingensis was the most ancient salmonid lineage. The divergence
time between E. lucius and salmonid fishes was 132.9 Mya, and the
divergence time between B. l. tsinlingensis and other salmonid
fishes was 41.4 Mya (Figure 4C ). Because of the Ss4R event in
salmonids, we assessed the expanded gene families in salmonid lines andB. l. tsinlingensis , respectively. GO and KEGG enrichment
analysis of salmonid
expanded
gene families indicated that most genes were related to protein binding,
kinase activity, transferase activity, Toll signaling pathway, receptor
activity, Glycolysis / Gluconeogenesis, citrate cycle,
Pentose
phosphate pathway, and Fatty acid biosynthesis,
which
indicates that metabolic processes in salmonids may differ from those in
other fishes after the Ss4R event; the larger body size of salmonids
might reflect differences in metabolic processes
(Table
S15-S16 ). The GO and KEGG enrichment analysis of B. l.
tsinlingensis expanded gene families revealed that most genes were
related to the regulation of apoptotic process, cell death, insulin
receptor binding, lysozyme activity, biological regulation, ascorbate
and aldarate metabolism, lipopolysaccharide biosynthesis, and mismatch
repair, which indicates that the immune system of B. l.
tsinlingensis might differ from that of other fishes (Table
S17-S18 ). These unique expanded gene families can help us better
understand the biology B. l. tsinlingensis and aid its
conservation.