DOI: 10.6084/m9.figshare.19915375
title: Additional file 1 of The functional evolution of termite gut microbiota

description: Additional file 1: Table S1. Termite samples sequenced in the study. Table S2. Relative abundance of family-level prokaryotic taxa inferred from gut metagenome and 16S rRNA amplicon data of 74 termite samples. The prokaryotic taxonomy was determined with GTDB for marker genes and with SILVA for 16S rRNA data. The relative abundance was clr-transformed to account for differences in sequencing method and sequencing depth among metagenome samples. Table S3. Taxonomic distribution of major bacterial and archaeal groups based on relative abundance of 40 single-copy marker genes. We analyzed the marker genes present in contigs longer than 1000 bps in &gt;5% of gut metagenomes. The relative abundance is represented as transcripts per million (TPM). Table S4. Moran's I phylogenetic autocorrelation index calculated for 123 prokaryote families. Significance was assessed with 9999 random permutations. P-values &lt;0.05 are indicated by asterisks. Table S5. Relative abundance of prokaryotic CAZymes in gut metagenomes with upward of 10000 contigs longer than 1000 bps. Relative abundance is given as transcripts per million (TPM). Table S6. Moran's I phylogenetic autocorrelation index calculated for 211 prokaryotic CAZymes present in more than 10% of gut metagenomes. Significance was assessed with 9999 random permutations. P-values &lt;0.05 are indicated by asterisks. Table S7. Phylogenetic ANOVA calculated for 211 prokaryotic CAZymes present in more than 10% of gut metagenomes. Significance was assessed with 9999 random permutations. P-values of phylogenetic ANOVA and pairwise comparisons were adjusted at 5% false discovery rate (FDR). The relative abundance of each CAZyme for the four termite groups are indicated by mean TPM values. Significance of pairwise comparisons between termite groups are indicated by asterisks (* p &lt; 0.05; ** p &lt; 0.01; *** p &lt; 0.001). Table S8. Phylogenetic ANOVA comparing the taxonomic origin of the 19 prokaryotic CAZymes found in 10% of gut metagenomes and embedded in contigs longer than 5000 bps. Significance was assessed with 9999 random permutations. The relative abundance of each CAZyme for the four termite groups are indicated by mean TPM values. Significance of pairwise comparisons between termite groups are indicated by asterisks (* p &lt; 0.05; ** p &lt; 0.01; *** p &lt; 0.001). Table S9. Information about the 654 MAGs reconstructed in this study. Table S10. Distribution of polysaccharide utilization loci (PULs) across the MAGs. PULs with at least one GH and Bacteroidota PULs with at least one susCD complex are shown. MAGs containing PULs with all the components are highlighted in grey. Table S11. Moran’s I phylogenetic autocorrelation index and phylogenetic ANOVA performed on the genes involved in the final steps of the lignocellulose digestion in the gut of termites. For genes composed of multiple subunits, all subunits were summed together. Significance was assessed with 9999 random permutations. P-values were adjusted at 5% false discovery rate (FDR). The relative abundance of each gene for the four termite groups are indicated by mean TPM values. Significance of pairwise comparisons between termite groups are indicated by asterisks (* p &lt; 0.05; ** p &lt; 0.01; *** p &lt; 0.001). Table S12. Distribution of genes involved in reductive acetogenesis among MAGs. Distribution is shown as presence (1) and absence (0). Asterisks indicate genes that were annotated using BLASTx search against the AnnoTree database (perc. identity &gt;60%, align. length &gt;100 aa). Other genes were annotated using HMM search against the KEGG or Pfam databases. [FeFe] hydrogenase GroupA4 were annotated using the Hyddb webtool followed by manual inspection of the conserved motifs. The total number of HycB3 (PF13247) found in each MAG is shown. MAGs with almost complete reductive acetogenesis pathway (&gt;5 genes) and HDCR complex are highlighted in grey. Table S13. Relative abundance of methyl-coenzyme M reductase (mcrABG) gene complex present in metagenome contigs longer than 5000 bps. Contigs were annotated using BLASTx search against the GTDB database. Relative abundance of the gene family is shown as raw TPM. Table S14. Distribution of genes involved in methanogenesis among MAGs. Distribution is shown as presence (1) and absence (0). Asterisks indicate genes that were annotated using BLASTx search against the AnnoTree database (perc. identity &gt;60%, align. length &gt;100 aa). Other genes were annotated using HMM search against the KEGG or Pfam databases. Highlighted MAGs have a complete Methanogenesis pathway. Table S15. Distribution of genes involved in sulfate reducing among MAGs. Distribution is shown as presence (1) and absence (0). Asterisks indicate genes that were annotated using BLASTx search against the AnnoTree database (perc. identity &gt;60%, align. length &gt;100 aa). MAGs with complete sulfate reducing pathway are highlighted. Table S16. Genes involved in nitrogen metabolism and fixation found in our MAGs. Distribution is shown as presence (1) and absence (0). Asterisks indicate genes that were annotated using BLASTx search against the AnnoTree database (perc. identity &gt;60%, align. length &gt;100 aa). MAGs with complete nitrogen fixation or dissimilatory nitrate reduction pathways are highlighted. Table S17. Contigs endowed with a NifHDKENB (nifHDKENB, vnfHDKENB, or anfHDKENB) gene complex found in gut metagenomes. The relative abundance is given as raw TPM. Table S18. Contigs endowed with a NifHDK (nifHDK, vnfHDK, or anfHDK) gene complex found in termite gut metagenomes. The relative abundance is given as raw TPM. Table S19. Fossil calibrations used to calibrate the time-calibrated tree of termites.