Figure 1.
Circular representation of the five replicons of the Methylobacterium oryzae CBMB20T genome.
The first circle from inside is the color-coded COG functional category and next black circle indicates the scale bar. The third and fourth circles indicate the GC skew and the GC content. Next vertical red bars denote tRNAs and the green bars the rRNA operons. In the next circle are predicted CDSs represented by 25 colors according to COG functional classification (Table S4), and outermost bars indicate genomic islands (Table S1).
Table 1.
General features of the Methylobacterium oryzae CBMB20T genome.
Figure 2.
Methylotrophy gene clusters of M. oryzae CBMB20.
The genetic loci for methylotrophy, surmounting to ca. 53 kb, are dispersed in the chromosome into seven clusters ranging from 2.74 to 19.18 kb in size and dozens of isolated genes. Gray arrows indicate the genes unrelated to methylotrophy. White arrows indicate the genes with unassigned function.
Figure 3.
Phylogenetic tree of the members of Methylobacterium whose genome sequences have been determined.
The amino-acid sequences of 36 broadly conserved proteins were concatenated and aligned with MUSCLE, from which a neighbor-joining tree was constructed using MEGA 5. Methylocella silvestris BL2 (CP001280) was used as the out-group. Colored circles indicate the kinds of proteins that are known to promote plant growth.
Figure 4.
Comparison of the COG and subsystem assignments among completely sequenced Methylobacterium species.
Color key indicates the relative abundance (Table S4). Heat maps were constructed using R script.
Figure 5.
Flower plot of the core genome and strain-specific genes of genome-sequenced Methylobacterium strains.
The number in the center circle indicates the core genes of completely sequenced Methylobacterium strains and the numbers in the floral leafs indicate the number of strain specific CDSs, respectively.
Table 2. Number of shared genes and the pan-genome of Methylobacterium species.
Table 3.
COG and subsystem comparison of strain-specific CDSs.
Figure 6.
Methylotrophy and adaptation to the phyllosphere.
Its genome contains an assortment of genes that may contribute to adaption to the phyllosphere, interaction with plants, and promotion of plant growth. H4F, tetrahydrofolate; H4MPT, tetrahydromethanopterin; MFR, methanofuran; PGA, phosphoglycerate; PEP, phosphoenolpyruvate; OAA, oxaloacetate; EMC, ethylmalonyl-CoA pathway; TCA, tricarboxylic acid cycle; ACC, 1-aminocyclopropane-1-carboxylate; AccD, 1-aminocyclopropane-1-carboxylate deaminase; DMAPP, dimethylallyl diphosphate; MiaA, tRNA isopentenylpyrophosphate transferase; PQQ, pyrroloquinoline quinone.