Fig. 3

Gene family dynamics and functional enrichment in molluscan evolution. (a) Phylogenetic analysis and gene family evolution of 11 molluscan species. Tree topology with estimated divergence times (million years ago, MYA, including range) is shown next to each lineage (blue). Number of expanded (green) and contracted (red) gene families shown next each branch. The right panel illustrates the distribution of gene families among 11 molluscan species. It shows the number of shared single-copy genes (red), which are present in all analyzed genomes but exist in only one copy per individual genome; shared multiple-copy genes (yellow), which are present in all analyzed genomes and exist in multiple copies in individual genomes; genes found only in Argopecten species (green); genes found in Pectinidae species (purple); genes found only in the corresponding species (blue); and other species-combination of orthologous genes (grey). (b) Venn Diagram graph of orthologous gene families shared/not shared among 11 molluscan species. (c) Enriched KEGG pathway analysis for expanded gene families in Argopecten irradians. The bubble plot illustrates the top 20 enriched pathways, where the bubble size reflects the number of genes and the color gradient (-log₁₀(P-value)) indicates the significance of the enrichment.