The genome of Rhizobium leguminosarum has recognizable core and accessory components

Young, J. Peter W.; Crossman, Lisa; Johnston, Andrew; Thomson, Nicholas R.; Ghazoui, Zara; Hull, Katherine H; Wexler, Margaret; Curson, Andrew R. J.; Todd, Jonathan D.; Poole, Philip S.; Mauchline, Tim H.; East, Alison K.; Quail, Michael A.; Churcher, Carol; Arrowsmith, C.; Cherevach, Inna; Chillingworth, Tracey; Clarke, Kay; Cronin, Ann; Davis, Paul A.; Fraser, Audrey; Hance, Zahra; Hauser, Heidi; Jagels, Kay; Moule, Sharon; Mungall, Karen; Norbertczak, Halina; Rabbinowitsch, Ester; Sanders, Mandy; Simmonds, Mark; Whitehead, Sally; Parkhill, Julian

doi:10.1186/gb-2006-7-4-r34

Cited by 503 publications

(275 citation statements)

References 94 publications

(109 reference statements)

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“…In contrast, the 16S rRNA gene-based phylogeny shows Bradyrhizobium japonicum (cluster C) close to Caulobacter crescentus (cluster D) and distant from Mesorhizobium loti (cluster B). Moreover, within cluster B, the DnaJ-based phylogeny shows Ensifer meliloti closer to Agrobacterium tumefaciens and Mesorhizobium loti closer to Brucella suis, which is in full agreement with the phylogeny proposed by Young et al (2006) based on the concatenated sequences of 638 proteins (the present study uses Brucella suis rather than Brucella melitensis) and with the multilocus tree of life presented by Ciccarelli et al (2006), and not concordant with the 16S rRNA gene phylogeny. Therefore, the possible HGT origin of dnaJ from Agrobacterium tumefaciens (cluster B) suggested by the G+C content analysis was not confirmed.…”

Section: The Alphaproteobacteriasupporting

confidence: 79%

“…Gupta & Sneath (2007) studied just proteobacteria, using the amino acid sequences of 10 protein-coding genes. A larger number of proteins (648) was used by Young et al (2006) to generate a phylogeny that shows the relationship of Rhizobium leguminosarum and its close relatives with completely sequenced genomes. These studies indicate that a large amount of core gene sequence information produces strongly supported and more resolved phylogenies, frequently in disagreement with 16S rRNA gene-based phylogenies.…”

Section: Introductionmentioning

confidence: 99%

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dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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In the past, bacterial phylogeny relied almost exclusively on 16S rRNA gene sequence analysis. More recently, multilocus sequence analysis has been used to infer organismal phylogenies. In this study, the dnaJ chaperone gene was investigated as a marker for phylogeny studies in alphaproteobacteria. Preliminary analysis of G+C contents and G+C3s contents (the G+C content of the synonymous third codon position) showed no clear evidence of horizontal transfer of this gene in proteobacteria. dnaJ-based phylogenies were then analysed at three taxonomic levels: the Proteobacteria, the Alphaproteobacteria and the genus Mesorhizobium. Dendrograms based on DnaJ and 16S rRNA gene sequences revealed the same topology described previously for the Proteobacteria. These results indicate that the DnaJ phylogenetic signal is able to reproduce the accepted relationships among the five classes of the Proteobacteria. At a lower taxonomic level, using 20 alphaproteobacteria, the 16S rRNA gene-based phylogeny is distinct from the one based on DnaJ sequence analysis. Although the same clusters are generated, only the topology of the DnaJ tree is consistent with broader phylogenies from recent studies based on concatenated alignments of multiple core genes. For example, the DnaJ tree shows the two clusters within the Rhizobiales as closely related, as expected, while the 16S rRNA gene-based phylogeny shows them as distantly related. In order to evaluate the phylogenetic performance of dnaJ at the genus level, a multilocus analysis based on five housekeeping genes (atpD, gapA, gyrB, recA and rplB) was performed for ten Mesorhizobium species. In contrast to the 16S rRNA gene, the DnaJ sequence analysis generated a tree similar to the multilocus dendrogram. For identification of chickpea mesorhizobium isolates, a dnaJ nucleotide sequence-based tree was used. Despite different topologies, 16S rRNA gene-and dnaJ-based trees led to the same species identification. This study suggests that the dnaJ gene is a good phylogenetic marker, particularly for the class Alphaproteobacteria, since its phylogeny is consistent with phylogenies based on multilocus approaches. INTRODUCTIONThe phylum Proteobacteria is composed of five classes, the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria (Garrity et al., 2005;Stackebrandt et al., 1988). By the end of 2008, more than 380 complete genomes of proteobacteria were available in public databases (http://www. ncbi.nlm.nih.gov/genomes/lproks.cgi). Alphaproteobacteria exhibit an enormous diversity in their morphological and metabolic characteristics and the class is presently recognized solely as a clade in the 16S rRNA gene-based phylogeny (Stackebrandt et al., 1988). Based on 16S rRNA gene trees, the Alphaproteobacteria has been divided into seven orders: Caulobacterales, Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Parvularculales (Kersters et al., 2006). The Alphaproteobacteria includes important bacteria tha...

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Section: The Alphaproteobacteriasupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

View full text Add to dashboard Cite

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“…Rhizobial genomes are subdivided into genome regions specific for their life stages, with chromosomal loci expressed during free-living phases in the soil and symbiosis loci expressed inside of host cells [13,14]. Symbiosis loci required for host nodulation and nitrogen fixation are clustered onto large plasmids or genomic islands [15][16][17][18][19], that can be transferred among lineages, presumably via conjugation [20][21][22]. Non-nodulating rhizobia are also common [23,24], and these strains often lack some or all of the characterized symbiosis loci [23][24][25][26][27][28].…”

Section: Introductionmentioning

confidence: 99%

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

et al. 2015

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The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory Bsymbiosis island^loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypeswith a single Bepidemic^haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and nonsymbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.

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“…In addition to symbiotic plasmids, several rhizobial strains also contain one or more smaller, accessory plasmids, also termed non-symbiotic plasmids (Mercado-Blanco and Toro, 1996;Gonzalez et al, 2006;Stiens et al, 2006;Young et al, 2006). Some of these plasmids have been shown to transfer between populations of indigenous rhizobia (Mercado-Blanco and Toro, 1996).…”

Section: Introductionmentioning

confidence: 99%

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

et al. 2008

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In silico, physiological and in planta analyses were used to characterize pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1, and assess its potential ecological function under free-living and symbiotic growth conditions. Sequence analysis revealed the presence of an uptake hydrogenase system, a repABC family plasmid replication module and open reading frames encoding type IV secretion system, TraI and TraR autoinducer proteins and several copper resistance-related proteins. Bradyrhizobium sp. BTAi1 was capable of growing in 200 mg l À1 CuCl 2 . In contrast, the closely related, plasmid-free Bradyrhizobium sp. strain ORS278 could not grow at copper concentrations exceeding 100 mg l À1 . The plasmid-localized hydrogenase genes were phylogenetically distinct from those typically found in other rhizobial species, and were most related to hup genes from Thiobacillus denitrificans. The induction of the plasmid-borne hydrogenase genes during symbiosis was significantly lower than the two chromosomal-borne hydrogenase clusters. CHEF-pulsed-field gel electrophoresis was used for a comprehensive analysis of the diversity, abundance and genetic composition of accessory plasmids in other Bradyrhizobium strains. Plasmids were detected in 11 of 46 (23.9%) geographically diverse Bradyrhizobium japonicum and Bradyrhizobium elkanii strains, isolated from the United States, China and Thailand. Plasmid size was heterogeneous, ranging from 75 to 330 kb, with only two strains (DASA01244 and DASA01265) harboring plasmids with identical (240 kb) size. None of the plasmids harbored nodulation or hydrogenase genes. Taken together, our results indicate that while plasmids having ecologically significant functions may be detected in Bradyrhizobium sp. strains, they lack genes necessary for symbioses with legumes.

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The genome of Rhizobium leguminosarum has recognizable core and accessory components

Cited by 503 publications

References 94 publications

dnaJ is a useful phylogenetic marker for alphaproteobacteria

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

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