Positive selection analysis
To further uncover the genomic characteristics of Chinese bahaba, we
performed a positive selection analysis. Using 4,594 single-copy gene
families, we identified 47 positive selection genes (PSGs). we also
conducted KEGG and GO enrichment analyses, yet no significant enrichment
results were obtained. Nonetheless, we remain interested in a few genes,
such as tcn2 , which participates in the KEGG pathway of cobalamin
transport and metabolism, cd44 , which is related to the
hematopoietic cell lineage. slc24a4 is in the GO term, calcium,
potassium:sodium antiporter activity.
In addition, we performed positive selection analyses and multiple
sequence comparisons for otolith-associated genes in the Sciaenidae
fish. We initially analysed these genes using D. rerio, X.
maculatus, G. aculeatus, C. lucidus, and L. crocea . After multiple
sequence comparisons and structural domain identification, we
constructed an evolutionary tree of these genes and labelled the
structural domains of the corresponding proteins, but did not find the
presence of significant positive selection sites. We suspected that this
was related to the close genetic relationship of these fishes.
Therefore, we introduced European sea bass (Dicentrarchus labrax )
and fugu (Takifugu rubripes ) for comparison, which are more
distantly related to Chinese Bahaba. After multiple sequence comparisons
and Branch-site model analysis, we found that only the sparcl1 gene was significantly affected by positive selection in the Sciaenidae
fish (Table S2 ). Therefore, we focused on the sparcl1 gene and constructed an evolutionary tree. The evolutionary tree
revealed that the sparcl1 genes of the Chinese bahaba and large
yellow croaker are the closest relatives. Meanwhile, in the analysis of
the structural domains of the Sparcl1 protein, we found that the
structural domains of the gene were conserved, mainly consisting of
three parts: KACAL FS superfamily, EFH SPARC EC superfamliy and FOLN
superfamily (Fig. 4 ). It was revealed that a total of six amino
acid sites in the sparcl1 gene in the large yellow croaker and
Chinese bahaba may have undergone positive selection. They had serine
(S) at positions 122 and 125, glutamic acid (E) at position 124,
threonine (T) at positions 123 and 160, proline (P) at position 128, and
glutamine (Q) at position 141. Among these six sites, the four sites in
the top order had the highest confidence and all four sites were at the
same position (Fig. 5 ).