Fig. 4

Gene-scale metapangenomic analysis suggests candidate gene-level drivers of habitat adaptation. a Gene-level coverage of Rothia sp. E04. Units along the angular axis are R. sp. E04 genes, arranged in order found in R. sp. E04 with contigs joined arbitrarily. The innermost ring labels whether each gene was shared with all of R. mucilaginosa group 1 (pink), only between the BM-enriched strains R. spp. E04 and C03 (black; also shown with black lines outside figure), or otherwise (gray). The innermost 30 layers show coverage of each gene for 30 TD metagenomes with the highest coverage; middle 30, BM metagenomes; outer 30, SUPP metagenomes. Each layer’s y-axis shows coverage by an individual sample, with y-axes scaled independently for each layer. The three outermost layers show whether genes were determined as environmental accessory (red) or core in TD (blue), BM (violet), or SUPP (green). Arrowheads show examples of gene abundance patterns: uniformly low-to-absent coverage across metagenomes (empty black) vs stochastically abundant but typically environmentally accessory (filled black). b Nucleotide-level coverage for a 20-kb contiguous stretch of R. sp. E04’s genome that includes a candidate gene driver of the BM adaptation, GC_00004770. This stretch is shown by the labeled grey arc in a. Each trace shows a single sample’s coverage, colored according to its oral site. Black bars show the mean Shannon entropy for variant sites covered at least 10x. Gray boxes above the SUPP traces mark genes, with GC_00004770 highlighted in black. c Table of the 22 gene clusters unique to R. sp. E04 and R. sp. C03 (also marked with black ticks in panel a). The columns labeled “Environmental Core/Accessory” show the fraction of genes in each gene cluster that are core (colored according to that habitat’s color) or environmentally accessory (red). The corresponding Pfam function is listed for gene clusters for which a function could be predicted. The gene clusters environmentally core in BM and SUPP but not in TD are bolded