Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti
Marco Galardini,Alessio Mengoni,Matteo Brilli,Francesco Pini,Antonella Fioravanti,Susan Lucas,Alla Lapidus,Jan Fang Cheng,Lynne Goodwin,Sam Pitluck,Miriam Land,Loren Hauser,Tanja Woyke,Natalia Mikhailova,Natalia Ivanova,Hajnalka E. Daligault,David Bruce,J. Chris Detter,Roxanne Tapia,Cliff Han,Hazuki Teshima,Stefano Mocali,Marco Bazzicalupo,Emanuele G. Biondi,Emanuele G. Biondi +24 more
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TLDR
The extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity of S. meliloti strains AK83 and BL225C, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.Abstract:
Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains. With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains. In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.read more
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CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes
TL;DR: Contiguator as discussed by the authors is a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting to finish multipartite genomes.
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Legume growth-promoting rhizobia: an overview on the Mesorhizobium genus.
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The bacterial pangenome as a new tool for analysing pathogenic bacteria
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Journal ArticleDOI
Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies
Masayuki Sugawara,Brendan Epstein,Brian D. Badgley,Tatsuya Unno,Lei Xu,Jennifer Reese,Prasad Gyaneshwar,Roxanne Denny,Joann Mudge,Arvind K. Bharti,Andrew Farmer,Gregory D. May,Jimmy E. Woodward,Claudine Médigue,David Vallenet,Aurélie Lajus,Zoé Rouy,Betsy M. Martinez-Vaz,Peter Tiffin,Nevin D. Young,Michael J. Sadowsky +20 more
TL;DR: The results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant, and the diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.
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micropan : an R-package for microbial pan-genomics
TL;DR: An R package for the study of prokaryotic pan-genomes is presented and parts of the package are demonstrated on a data set for the gram positive bacterium Enterococcus faecalis.
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