Fig. 3.
Distribution of host- and lineage-specific genes. A Presence and absence of gene families specific to different lineages or hosts (yellow, present; black, absent). Lineage- and host-specific genes were analyzed using Scoary [33]. Gene families with sensitivity and specificity both above 70% and Bonferroni-adjusted p-value less than 0.05 were included. B Distribution of key functional gene clusters and genes among different lineages. Five categories of genes are shown in different colors, from left to right: biofilm formation (blue), acid resistance (turquoise), metabolism (gray), oxidative stress (green), and CRISPR-Cas and phage (purple). The function of the genes are described as follows: bfrKR, two-component regulatory system; cemKR, two-component regulatory system; asp2, accessory Sec system protein Asp2; secA, protein translocase subunit SecA2; Lr70894, secA2 operon component; lev, levansucrase; Lr70134, Lr70131, EDX43652, EDX42265, large surface proteins (Lsp) containing LPXTG cell wall anchoring motif; gadB, glutamate decarboxylase; gls1, gls2, gls3, the 3 glutaminases; ure, urease gene cluster for urea metabolism; pdu and cbi, part of the pdu-cbi-cob-hem gene cluster that mediates 1,2-propanediol and glycerol utilization, and cobalamin biosynthesis; manA, mannose-6-phosphate isomerase; ERG8, phosphomevalonate kinase; glpT, glycerol-3-phosphate transporter; PAD, phenolic acid decarboxylase; frc, formyl-coenzyme A transferase; rib, gene cluster for riboflavin biosynthesis; cit, citrate lyase cluster; yvyI, mannose-6-phosphate isomerase YvyI; SDR, short-chain dehydrogenases/reductases; thrBC, threonine biosynthetic cluster; cpnA, cyclopentanol dehydrogenase; rtpR, adenosylcobalamin-dependent ribonucleoside-triphosphate reductase; moaA/moaAC/moaDE/mogA/mobAB, genes for molybdenum cofactor (Moco) biosynthesis; nreB, oxygen sensor histidine kinase NreB; pnbA, nitroreductase-like family protein; tpx, redoxin domain protein; HMA, heavy metal translocating P-type ATPase; cad, cadmium resistance transporter; cas1, CRISPR-Cas system; gp36, phage phi-C31 major capsid gp36-like protein