Additional file 2 of Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

Additional file 2: Table S4: GO enrichment analysis. The enrichment analysis, using topGo, of genes identified in M. mercenaria in this study but not found in M. mercenaria YKG (3 first columns) and genes found in M. mercenaria YKG but not in our M. mercenaria assembly (3 last columns). Table S5: Functional annotation and gene duplication. For each gene annotated in this study, gene duplication events (0: “Not duplicated” 1:"dispersed duplication” 2:"proximal duplication” 3:"tandem duplication” 4:"segmental duplication”), Gene Ontology identification and the three first best matches on NR are listed. Table S6: GO enrichment in duplicated genes. GO enrichment analysis using topGO was performed on the genes found duplicated within M. mercenaria genome. Results were sorted by p value. Table S7: Genes expanded in M. mercenaria across Bivalvia. Orthogroups gene counts across 20 genomes of Bivalvia with expanded genes in M. mercenaria. Ave being the mean of copies in each species. Expansion column: 1: genes expanded in M. mercenaria not detected in all other species. 2: Genes with copy numbers higher in M. mercenaria than the mean number of copies in all other species. 3: Genes with copy numbers higher in M. mercenaria than the mean number of copies in all Venerida species. Table S8: TNF containing domain genes. List of all M. mercenaria genes found in orthogroups containing TNF domains. The CDS start position, the type of duplication (0: “Not duplicated” 1:"dispersed duplication” 2:"proximal duplication” 3:"tandem duplication” 4:"segmental duplication”), the orthogroup ID, the best three first matches on NR, the principal and the number of transmembrane domain and the protein length are reported. Colors represent orthogroups used for the phylogenetic tree (Fig. 4).