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).
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.