Within the group of closely related strains RtTA1, R. leguminosarum bv. viciae 3841 (Rlv), R. etli CFN42 (Rhe),

RltWSM2304 and RltWSM1325 clusters of replicons carrying the most similar replication systems can be distinguished. They comprise pRleTA1d-pRL12-p42f-pRLG201-pR132501 and pRleTA1b-pRL11-p42e-pRLG202-pR132502, respectively. Therefore, detection of positive hybridization signals with probes derived from rep genes of RtTA1 chromid-like replicons (i.e. pRleTA1b or pRleTA1d) to any of the replicons of the sampled strains allowed regarding those as a chromid-like. Based on the similarity of replication-partition genes detected in our assays, we divided the replicons of the studied strains into three genome compartments: chromosome, 3-Methyladenine in vivo chromid-like and ‘other plasmids’ (i.e. those replicons which gave a hybridization signal with molecular probes originating from repA and repC genes of pRleTA1a or pRleTA1c, as well as those that gave no signal with any rep probes of RtTA1 replication genes). The compartment designated ‘other plasmids’ also comprised pSym. Such replicon division was taken into consideration in the subsequent analyses of distribution of other markers in the studied strains. SB-715992 order Variability of chromosomal and plasmid marker location In further studies, the extent of gene content diversity in the sampled nodule isolates was examined. We aimed to estimate whether, besides repA and repC displacement

events, we could demonstrate changes in the location

of the chromosomal and plasmid genes. The same experimental approach was used, i.e. a series of Southern hybridizations with different genes with a well-defined chromosomal or plasmid location in RtTA1 (Table 1) [36]. For assays of chromosomal marker variability, essential bacterial genes were chosen: rpoH2, dnaK, dnaC, rrn, lpxQ as well as genes that are not essential or with unspecified essentiality but chromosomal in RtTA1, i.e. bioA, stbB, exoR, pssL (Pss-I) and rfbADBC (Pss-V) (Table 1). In addition, location of fixGH genes was assayed, even though they click here are known to be plasmid located on the sequenced RltWSM2304, RltWSM1325 [33, 34], Rlv [6] and Rhe [5] genomes, but chromosomal in RtTA1 [36]. A majority of the studied genes (rpoH2, dnaK, dnaC, rrn, lpxQ, bioA, stbB, exoR and pssL) were located on the chromosome in all the sampled strains, showing considerable conservation of chromosomal markers (Figure 3). Exceptionally, the Pss-V region was identified on the chromosome of the K3.6, K5.4 and RtTA1 but it was missing in the other strains (Figure 3) Moreover, fixGH symbiosis-related genes, which were chromosomal in the RtTA1, K3.6, K4.15 and K5.4 strains, were located mainly in the genome compartment designated as ‘other plasmids’ (pSym to be exact) in the remaining strains. The variable location of fixGH genes which were found on the chromosome, pSyms and chromid-like replicons (K12.