Figure legends
Figure 1. Pipeline for the construction of the gene catalogue of Rhinopithecus gut microbiome (RGC).Shotgun sequencing reads for fecal samples from R. roxellana ,R. bieti and R. strykeri individuals were independently processed. We generated three non-redundant gene-sets and merged them into an integrated reference gene catalogue of the SNMs gut microbiome (RGC).
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Figure 2. Annotation of the RGC . A . Breakdown of taxonomic annotations for the RGC. B . The top 11 phyla in the RGC. Firmicutes and Bacteroidetes are the main two phyla in the RGC.C . The top 20 genera in the RGC. Clostridium is the main genus in the RGC. D. Number of shared microbiome features among SNMs at different frequency thresholds for the number of genes (black), COGs (pink), genera (orange), phyla (blue), KOs (purple) and CAZymes (yellow). The percentages of shared items and animals are represented on the y and x axes, respectively. The absolute numbers for each item are indicated at the intercept between the percentages of items and animals at the thresholds of 60% and 100%. Fewer than 2% of genes (207,635 genes) were shared by 60% of individuals, while approximately 36.5% of the KO functions (2,943) were shared by 60% of individuals, suggesting redundancy of genes for similar functions.
Figure 3. Comparisons of the RGC with the catalogues of ruminants and monogastric animal. A. The number of non-redundant genes in 12 mammalian species. B and C . Alpha diversity (Shannon index) at the genus, and KO function levels. Data are shown as box plots. The horizontal lines indicate the medians, and the whiskers indicate the lowest and highest points within 1.5× the interquartile ranges into the lower and upper quartiles, respectively. Coloured circles at the bottom indicate significance based on the relative index of each cohort according to the Wilcoxon rank-sum test. *P < 0.05, **P < 0.01, ***P< 0.001. D. Comparison of the host phylogeny tree (right panel; assembled using http://timetree.org/) and their gut microbiome hierarchical tree (upper left panel). E. PCoA plot of the gut microbiome composition in the 12 species at the genus level. F.PCoA plot of the gut microbiome composition in the 12 species at the KO function level.
Figure 4. Genera and CAZy terms differentially represented among ruminant animals, SNMs (ruminant-like animals) and monogastric animals (LEfSe). A. LEfSe test at genus level (LDA>0.4, P<0.05). Red circle: enriched in SNMs, green circle: enriched in ruminant animals, yellow circle: enriched in monogastric animals. B. LEfSe test at the CAZy level. Red box: enriched in SNMs, green box: enriched in ruminant animals, yellow box: enriched in monogastric animals. Text in bold: enriched in GH families.