Table 1.
Paenibacillus strains used in study.
Table 2.
Genomic features of Paenibacillus strains.
Figure 1.
Genomic diversity of strains in the genus Paenibacillus.
Each strain is represented by an oval that is colored: N2-fixing strains (red), non- N2-fixing strains (purple). The number of orthologous coding sequences (CDSs) shared by all strains (i.e., the core genome) is in the center. Overlapping regions show the number of CDSs conserved only within the specified genomes. Numbers in non-overlapping portions of each oval show the number of CDSs unique to each strain. The total number of protein coding genes within each genome is listed below the strain name.
Figure 2.
Functional classification of gene content of the 31 Paenibacillus strains.
(A) Profiles of Cluster of Orthologous Groups (COG) showing percentage of genes in each category out of total annotated genes. Taxa from inside of circle to outside of circle are from Paenibacillus sp. JDR 2 (top in the strain list) to P. sabinae T27 (down in the strain list). (B) Profiles of COG showing function categories for genes in core genomes. Taxa from inside of circle to outside of circle are from Paenibacillus sp. JDR 2 (top in the strain list) to P. sabinae T27 (down in the strain list).
Figure 3.
Organization of nif, vnf, anf and nif-like genes in N2-fixing Paenibacillus strains.
nif, vnf, anf and nif-like genes are marked with different colors. The 9 nif genes nifBHDKENXhesAnifV are contiguous within Sub-group I and there is a orf between nifX and hesA within Sub-group II.
Figure 4.
Comparison of G+C contents of the nif clusters with those of the average of the chromosomal genomes.
Figure 5.
Synteny of the chromosomal regions flanking the nif gene cluster among each sub-group.
(A) nif clusters of Sub-group I. (B) The chromosomal regions of non-N2-fixing strains corresponding to those flanking the nif gene cluster of Sub-group I. (C) nif clusters of Sub-group II.
Figure 6.
Bayesian inferred phylogenetic tree of concatenated NifHDK homologs.
The interior node values of the tree are clade credibility values, values lower than 100% are indicated. Branches are colored blue (Mo-nitrogenase, Nif), green (V-nitrogenase, Vnf), purple (Fe-nitrogenase, Anf), light blue (uncharacterized homolog), dark yellow (uncharacterized nitrogenase). The text colored red was Paenibacillus.
Figure 7.
Maximum-likelihood phylogenetic tree of Paenibacillus strains and the 4 possible evolutionary pathways of nitrogen fixation in Paenibacillus.
The tree was constructed based on 275 single-copy core proteins shared by the 31 Paenibacillus genomes and the rooting strain B. subtilis 168. Four likely pathways are marked with number 1–4.
Figure 8.
Maximum-likelihood phylogenetic tree of Mo-, Fe- and V-nitrogenases and nitrogenase-like sequences.
Nif/Vnf/AnfH, Nif/Vnf/AnfD, Nif/Vnf/AnfK, Nif/Vnf/AnfH-like, Nif/Vnf/AnfD-like and Nif/Vnf/AnfK sequences were derived from the 15 N2-fixing Paenibacillus strains and other representative species.