DNA Sequence of the Common Nodulation Genes of<i>Bradyrhizobium elkanii and</i>Their Phylogenetic Relationship to Those of Other Nodulating Bacteria

Dobert, Raymond C.; Breil, Brenda; Triplett, Eric W.

doi:10.1094/mpmi-7-0564

Cited by 78 publications

(53 citation statements)

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“…The nod genes of the soybean symbionts S. fredii and B. japonicum have been reported as being of the same lineage (Dobert et al, 1994), but the result was not supported by bootstrap analysis, as confirmed by more recent phylogenetic surveys inferred from nodA (Haukka et al, 1998) and nodC (Pre! vost et al, 2000) genes.…”

Section: Relationship Of Phylogeny Of Sym Genes To Host Specificitymentioning

confidence: 95%

“…On the other hand, lateral gene transfer of the Sym genes appears to be the most plausible hypothesis to explain cases of phylogenetic incongruence between Sym and housekeeping genes (Martinez-Romero & CaballeroMellado, 1996 ;Young & Haukka, 1996). Indeed, phylogenetic trees based on sequences of nod genes are generally not congruent with those based on 16S rDNA sequences, but the nod trees show some correlation with host plant range (Dobert et al, 1994 ;Lindstro$ m et al, 1995 ;Ueda et al, 1995 ;Haukka et al, 1998 ;Wernegreen & Riley, 1999). By contrast, the phylogeny of nifH genes, which encode the dinitrogenase reductase enzyme, has been reported as closely following that of 16S rRNA genes (Hennecke et al, 1985 ;Young, 1992 ;Dobert et al, 1994), despite some exceptions (Eardly et al, 1992).…”

Section: Figmentioning

confidence: 99%

“…Previous reports also indicated that some rhizobial strains, such as S. saheli, had different phylogenetic locations within rhizobia by comparing common nod gene and nifH evolutionary trees (Dobert et al, 1994 ;Haukka et al, 1998). Clearly, more work is needed to assess the linkage of nod and nif genes and the rest of the symbiotic genome.…”

Section: Relationship Of Phylogeny Of Sym Genes To Host Specificitymentioning

confidence: 99%

“…Similarly, the samples of soybean and lupin bradyrhizobial strains investigated in this study constituted heterogeneous 16S rDNA groups that were phylogenetically intermixed with each other and with bradyrhizobia isolated from other host legumes (Xu et al, 1995) harboured similar Sym genes. The B. elkanii strains had a specific Sym RFLP type, but former phylogenetic analyses had established that the common nodulation genes of B. japonicum and B. elkanii were closely related (Dobert et al, 1994 ;Ueda et al, 1995). However, further studies are necessary to investigate whether the Sym gene phylogeny is correlated with the 16S rRNA classification and host range within the Bradyrhizobium genus, which includes a wide variety of yet unclassified microsymbionts associated with many legumes.…”

Section: Relationship Of Phylogeny Of Sym Genes To Host Specificitymentioning

confidence: 99%

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Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts The GenBank accession numbers for the sequences reported in this paper are AF217261 through AF217272 for nodC and AF218126, AF275670 and AF275671 for nifH.

et al. 2001

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The nodC and nifH genes were characterized in a collection of 83 rhizobial strains which represented 23 recognized species distributed in the genera Rhizobium, Sinorhizobium, Mesorhizobium and Bradyrhizobium, as well as unclassified rhizobia from various host legumes. Conserved primers were designed from available nucleotide sequences and were able to amplify nodC and nifH fragments of about 930 bp and 780 bp, respectively, from most of the strains investigated. RFLP analysis of the PCR products resulted in a classification of these rhizobia which was in general well-correlated with their known host range and independent of their taxonomic status. The nodC and nifH fragments were sequenced for representative strains belonging to different genera and species, most of which originated from Phaseolus vulgaris nodules. Phylogenetic trees were constructed and revealed close relationships among symbiotic genes of the Phaseolus symbionts, irrespective of their 16S-rDNA-based classification. The nodC and nifH phylogenies were generally similar, but cases of incongruence were detected, suggesting that genetic rearrangements have occurred in the course of evolution. The results support the view that lateral genetic transfer across rhizobial species and, in some instances, across Rhizobium and Sinorhizobium genera plays a role in diversification and in structuring the natural populations of rhizobia.

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Section: Relationship Of Phylogeny Of Sym Genes To Host Specificitymentioning

confidence: 95%

Section: Figmentioning

confidence: 99%

Section: Relationship Of Phylogeny Of Sym Genes To Host Specificitymentioning

confidence: 99%

Section: Relationship Of Phylogeny Of Sym Genes To Host Specificitymentioning

confidence: 99%

See 2 more Smart Citations

Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts The GenBank accession numbers for the sequences reported in this paper are AF217261 through AF217272 for nodC and AF218126, AF275670 and AF275671 for nifH.

et al. 2001

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“…Several authors have constructed phylogenies based on nod gene sequences and have concluded that they are not congruent with those based on SSU rRNA (Gyorgypal, Kiss & Kondorosi, 1991;Dobert, Breil & Triplett, 1994;Lindstrom et al, 1995 a), For example, the nodABC and D genes of S, fredii and 5, meliloti are not closely related; they are closer to those of B. faponicum on the one hand and to R. leguminosarum biovars trifolii and viciae on the other. This makes sense in terms of their respective host plant ranges, and is more likely to reflect lateral transfer than convergent evolution since these genes, the so-called 'common nod genes' are not major determinants of host range.…”

Section: Symbiosismentioning

confidence: 99%

Diversity and phylogeny of rhizobia

1996

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SUMM.'iRYRhizobia are the bacteria that form nitrogen-fixing nodules on legumes. The current list of four rhizobium genera and 17 species is reviewed, with some comments on likely future developments in the taxonomy. Sequences of the small subunit ribosomal RNA (SSU or 16S rRNA) support the well-established subdivision of rhizobia into three genera: Rhizobium, Bradyrhizobium and Azorhizobium. These all lie within the alpha subdivision of the Proteohacteria, hut on quite distinct branches, each of which also includes many bacterial species that are not rhizobia. Rhizobium, by this definition, is still broad and poh'phyletic, so there have recently been suggestions that this genus should be split into four genera. SSU sequences may be tbe best phylogenetic tool we have, hut they are not an infallible guide to evolutionary relationships, particularly among closely related species: slow evolution, recombination, intraspecific variation and even intragenomic heterogeneity are all limitations that can be illustrated by examples from the rhizobia. It seems likely that the ability to form legume nodules was not present in the common ancestor of all rhizobia but that the nodulation genes were transferred hetween phylogenetically distinct bacteria, so that the phylogeny of nodulation genes will probably differ from that of the bacteria that carry them. Nitrogen fixation genes are often linked to nodulation genes, but they need not have the same evolutionary history.

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Matching population diversity of rhizobial nodA and legume NFR5 genes in plant–microbe symbiosis

Igolkina

Bazykin

Chizhevskaya

et al. 2019

Ecology and Evolution

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We hypothesized that population diversities of partners in nitrogen‐fixing rhizobium–legume symbiosis can be matched for “interplaying” genes. We tested this hypothesis using data on nucleotide polymorphism of symbiotic genes encoding two components of the plant–bacteria signaling system: (a) the rhizobial nodA acyltransferase involved in the fatty acid tail decoration of the Nod factor (signaling molecule); (b) the plant NFR5 receptor required for Nod factor binding. We collected three wild‐growing legume species together with soil samples adjacent to the roots from one large 25‐year fallow: Vicia sativa, Lathyrus pratensis, and Trifolium hybridum nodulated by one of the two Rhizobium leguminosarum biovars (viciae and trifolii). For each plant species, we prepared three pools for DNA extraction and further sequencing: the plant pool (30 plant indiv.), the nodule pool (90 nodules), and the soil pool (30 samples). We observed the following statistically significant conclusions: (a) a monotonic relationship between the diversity in the plant NFR5 gene pools and the nodule rhizobial nodA gene pools; (b) higher topological similarity of the NFR5 gene tree with the nodA gene tree of the nodule pool, than with the nodA gene tree of the soil pool. Both nonsynonymous diversity and Tajima's D were increased in the nodule pools compared with the soil pools, consistent with relaxation of negative selection and/or admixture of balancing selection. We propose that the observed genetic concordance between NFR5 gene pools and nodule nodA gene pools arises from the selection of particular genotypes of the nodA gene by the host plant.

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DNA Sequence of the Common Nodulation Genes ofBradyrhizobium elkanii andTheir Phylogenetic Relationship to Those of Other Nodulating Bacteria

Cited by 78 publications

References 0 publications

Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts The GenBank accession numbers for the sequences reported in this paper are AF217261 through AF217272 for nodC and AF218126, AF275670 and AF275671 for nifH.

Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts The GenBank accession numbers for the sequences reported in this paper are AF217261 through AF217272 for nodC and AF218126, AF275670 and AF275671 for nifH.

Diversity and phylogeny of rhizobia

Matching population diversity of rhizobial nodA and legume NFR5 genes in plant–microbe symbiosis

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