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A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.

ABSTRACT: BACKGROUND:Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria. DESCRIPTION:Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species. CONCLUSION:A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in this study as well as to generate new experiments. The next step will be expansion of the database to include other rhizobial species.

SUBMITTER: Azevedo H

PROVIDER: S-EPMC4460661 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.

Azevedo Helton H Lopes Fabricio F Silla Paulo P Hungria Mariangela M

BMC genomics 20150526

<h4>Background</h4>Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as ...[more]

PMID: 26040196

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Project description:Leishmaniasis is a debilitating infectious disease that has a variety of clinical forms. In China, visceral leishmaniasis (VL) is the most common symptom, and L. donovani and/or L. infantum are the likely pathogens. In this study, multilocus sequence typing (MLST) of five enzyme-coding genes (fh, g6pdh, icd, mpi, pgd) and two conserved genes (hsp70, lack) was used to investigate the phylogenetic relationships of Chinese Leishmania strains. Concatenated alignment of the nucleotide sequences of the seven genes was analyzed and phylogenetic trees were constructed using neighbor-joining and maximum parsimony models. A set of additional sequences from 25 strains (24 strains belong to the L. donovani complex and one strain belongs to L. gerbilli) were retrieved from GenBank to infer the molecular evolutionary history of Leishmania from China and other endemic areas worldwide. Phylogenetic analyses consolidated Chinese Leishmania into four groups: (i) one clade A population comprised 13 isolates from different foci in China, which were pathogenic to humans and canines. This population was subdivided into two subclades, clade A1 and clade A2, which comprised sister organisms to the remaining members of the worldwide L. donovani complex; (ii) a population in clade B consisted of one reference strain of L. turanica and five Chinese strains from Xinjiang; (iii) clade C (SELF-7 and EJNI-154) formed a population that was closely related to clade B, and both isolates were identified as L. gerbilli; and (iv) the final group, clade D, included Sauroleishmania (LIZRD and KXG-E) and was distinct from the other strains. We hypothesize that the phylogeny of Chinese Leishmania is associated with the geographical origins rather than with the clinical forms (VL or CL) of leishmaniasis. To conclude, this study provides further molecular information on Chinese Leishmania isolates and the Chinese isolates appear to have a more complex evolutionary history than previously thought.

Dataset Information

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.

Publications

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.

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