3.2 Genome annotation
About 357.31 Mb, accounting for 43.23 % of the assembled genome, were
identified as repetitive elements, including transposable elements, SSR,
and unknown elements. Class I and II transposable elements accounted for
23.34% and 12.59% of the assembled genome, respectively, and SSR
accounted for 0.59% (Table 1).
De novo , homology, and transcript-based methods were used to
predict the gene models. The expected results were integrated, and
36,738 non-redundant genes were obtained using the EVM software (Table
S4). The average exon length per gene was 2 kb (Figure 1c), the average
exon number per gene was 8.11, and the mean CDS length was 1,492.64 bp,
indicating a relatively fine consistency of the genome assembly. A total
of 1,829 pseudogenes, 450 miRNAs, 5,616 rRNAs, and 3,280 tRNAs were
annotated in the male O. bidens genome (Table 2). A total of
30,922 genes were functionally annotated using the GO, KEGG, KOG,
TrEMBL, and NR databases, representing 84.17% of the predicted genes
(Figure 2a). According to GO analysis, these annotated genes were
functional in cellular components, molecular functions, and biological
processes (Figure 2b). Of the annotated genes in the male O.
bidens genome assembly, 5,462 were orthologous to four species,D. rerio , L. rohita , C. carpio, and A.
graham (Figure 2c).
3.3 Genome phylogeny, expansion, and
contraction of gene families
In total, 4,350 single-copy orthologs and 18,271 gene families were
identified in the assembled genome of male O. bidens by
clustering homologous genes in S. rhinocerous , A. grahami ,L. rohita , D. rerio , O. latipes , T.
rubripes , C. carpio and G. aculeatus (Figure 3a). A
phylogenetic tree was constructed using these single-copy orthologues
(Figure 3b).
Together
with calibration times, the result showed that O. bidens was
divided from D. rerio at approximately 89.69 Mya, separated fromL. rohita at about 57.77 Mya, then isolated from A.
grahami at approximately 29.74 Mya, indicating a rapid differentiation
among these species.
A total of 496 and 305 gene families were significantly expanded and
contracted in the male O. bidens genome (p < 0.05),
respectively (Figure 3b). These gene families were mainly involved in 60
GO terms (Table S5; Figure S2), such as metabolic processes in
biological processes, organelles in cellular components, and catalytic
activity in molecular functions. The expanded and contracted gene
families were enriched in 76 KEGG pathways (Table S6; Figure S3), such
as the calcium signaling pathway, ABC transporters, GnRH signaling
pathway, melanogenesis, and adrenergic signaling in cardiomyocytes.