Genome evolution analysis
To investigate the phylogenetic relationships between the Chinese bahaba
and other fish species, we compared the Chinese bahaba genome with seven
other representative fish genomes for gene family identification and
constructed a phylogenetic tree. After comparison, we identified 21,346
gene families in totally. Of the total gene families, 13,846 gene
families were common to all reference fishes, and 818 gene families were
common to the four species in Sciaenidae. There are a total of 17,006
gene families shared by the Sciaenidae fishes and D.
undecimradiatus . Of these, 909 gene families were exclusively shared
between them. These genes may be unique and conserved to Perciformes
fishes (Figure S2 ).
On the basis of the single-copy gene families, we constructed a
phylogenetic evolutionary tree to further excavate the evolutionary
trajectory of Chinese bahaba. The evolutionary tree showed that the
Sciaenidae fishes separated from the zebrafish about 211.1 million years
ago (MYA) and from the perch fishes about 70.9 MYA. In contrast, the
Chinese bahaba were not fully separated from other Sciaenidae fishes as
a separate species until 10.7 MYA before present. Among the four species
of Sciaenidae fishes we selected, the large yellow croaker and the
Chinese bahaba have the closest genetic relationship. In reality, the
large yellow croaker is close to the Chinese bahaba in terms of size,
morphology, habit and food value, and its swim bladder is similar to the
Chinese bahaba in terms of its status and efficacy in the field of
medicine, which also side by side confirms the accuracy of the results
of our phylogenetic tree (Figure S3 ).
In order to find the unique genes that played a key role in separating
the Chinese bahaba from other fishes during the evolutionary process of
Chinese bahaba, we performed gene expansion and contraction analyses
(Fig. 2a ). Our main analytical goal focused on the evolutionary
differences within the family Sciaenidae. The analyses revealed that a
divergence occurred within the family Sciaenidae about 21.2 MYA, and
this divergence gave rise to 329 expansion gene families as well as 509
contraction gene families. In Chinese bahaba, we identified 447 expanded
and 1,248 contracted gene families. These expanded and contracted gene
families are evidence of the adaptation of the Chinese bahaba to its
environment and are the source of the unique traits that distinguish it
from the other fishes in the family Sciaenidae.
We performed GO and KEGG enrichment analysis of significantly expanded
gene families screened using café (Fig. 2b and c ). It
was found that these genes was significantly enriched in 32 GO terms. In
the Molecular Function classification, expansion genes are mainly found
to be related to hydrolase activity, peroxidase activity, transmembrane
transporter activity and scavenger receptor activity. In biological
process classification, expansion genes were mainly enriched in GO terms
such as immune response, antigen processing and presentation, and
biosynthetic process. In the cytological component classification,
expansion genes were less enriched, and their enrichment pathways were
mainly concentrated in myosin complex, supramolecular complex and
fibrinogen complex. In KEGG pathway analysis, we found that expansion
genes were enriched in immune system-related pathways such as CD
molecules, Lectins, and Pattern recognition receptors, suggesting that
the immune system of Chinese bahaba may have evolved with unique
mechanisms. In addition, some of the expanded genes were found in
metabolism and biosynthesis-related pathways such as Proteoglycans,
Ovarian steroidogenesis, Other glycan degradation and Arachidonic acid
metabolism.