FIGURE 4 The comparative genomic analysis of Corbicula
fluminea and other species. (A) Venn diagram of gene families betweenCorbicula fluminea and Crassostrea gigas, Lottia
gigantea, Bathymodiolus platifrons, and Crassostrea
virginica. (B) Distribution of multiple-copy orthologs, other
orthologs, single-copy orthologs, and unique genes in Corbicula
fluminea and the above four species. (C) Phylogenetic tree, divergence
time, and profiles of gene families that underwent expansion and
contraction in 11 species.
Combining the phylogenetic relationships, gene family evolution was
calculated by comparing the differences between ancestors and C.
fluminea . This analysis resulted in 851 gene families being
significantly expanded (P < 0.05) and 191 gene families being
significantly contracted (P < 0.05) in the Asian Clam genome
(Figure 4C, Supporting Information Table S10). The 851 expanded gene
families were clustered by 9,967 functional genes (Supporting
Information Table S11). The functional enrichment analysis on GO and
KEGG of those expanded genes identified 325 significantly enriched
(q-value < 0.01) GO terms (Supporting Information Table S12)
and 19 significantly enriched (q-value < 0.01) KEGG pathways
(Supporting Information Table S13, Supporting Information Figure S3).
Among 19 pathways, 9 pathways related to metabolite synthesis were given
attention, such as taurine and hypotaurine metabolism, drug metabolism,
O-Glycan biosynthesis and so on (Table 4). These results are helpful for
us to study and understand the characteristics of C. fluminea.