Article

A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria

The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
PLoS ONE (Impact Factor: 3.53). 02/2008; 3(7):e2567. DOI: 10.1371/journal.pone.0002567
Source: PubMed Central

ABSTRACT This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

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    • "that are highly expressed by rhizobia on plant roots [33]. On the other hand, plasmids are highly variable and confer adaptive traits, such as nodulation and nitrogen fixation in legumes [6] [8] [19] [26] [29] [38] [43] [49] [51], or they may be transferred between bacteria [30] [31] [40]. "
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    ABSTRACT: Genomics has provided data for defining bacterial-species limits from estimates of gene conservation, synteny, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH). Phylogenomic analyses that allowed a more accurate definition of rhizobial relationships showed two major superclades within the family Rhizobiaceae that corresponded to the Rhizobium/Agrobacterium and Shinella/Ensifer groups. Within the Rhizobium/Agrobacterium group, four highly-supported clades were evident that could correspond to distinct genera. The Shinella/Ensifer group encompassed not only the genera Shinella and Ensifer but also a separate clade containing the type strain of R. giardinii. Ensifer adhaerens (Casida AT) was an outlier within its group, separated from the rest of the Ensifer (formerly Sinorhizobium) strains. The phylogenomic analysis presented provided support for the revival of Allorhizobium as a bona fide genus within the Rhizobiaceae, the distinctiveness of Agrobacterium and the recently proposed Neorhizobium genus, and suggested that R. giardinii may be transferred to a novel genus. ANI reference values are becoming the gold standard in rhizobial taxonomy and are being used to recognize novel rhizobial lineages and species that seem to be biologically coherent, as shown in this study.
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    • "In contrast to chromosomes , plasmids are considered as usually poorly conserved, flexible and heterogeneous in size and gene content. Variations in the location of chromosomal and extrachromosomal genes can be observed even in small rhizobial populations (Crossman et al. 2008; Mazur et al. 2011b; López-Guerrero et al. 2012). Some of the rhizobial extrachromosomal replicons referred to as chromids are characterised by a plasmid-type replication system but differ from plasmids in their GC content and codon usage, which are similar to those of the chromosome. "
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    • "Several examples, particularly in the Rhizobiaceae family, demonstrate that a substantial portion of the existing genetic diversity is plasmid determined, where isolates of the same or closely related species share the same genomic core with plasmid-concentrated variation (Schofield et al. 1987; Gonzalez et al. 2003; Cervantes et al. 2011; Perez-Segura et al. 2013). One study compared isolates of two Rhizobium species and found that accessory plasmids were related by syntenic blocks of sequence, suggestive of high levels of recombination and genomic rearrangements within and between plasmids (Crossman et al. 2008). Similarly, a genome comparison between the two species A. tumefaciens C58 and Agrobacterium sp. "
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