Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

BMC Genomics

Research Article

Stefano Mocali¹  Samuel Pitluck²  Hajnalka Daligault²  Chris Detter²  Tanja Woyke²  Natalia Mikhailova²  David Bruce²  Susan Lucas²  Natalia Ivanova²  Hazuki Teshima²  Roxanne Tapia²  Cliff Han²  Jan-Fang Cheng²  Antonella Fioravanti³  Marco Galardini³  Marco Bazzicalupo³  Alessio Mengoni³  Francesco Pini³  Emanuele G Biondi⁴  Alla Lapidus⁵  Matteo Brilli⁶  Lynne Goodwin⁷  Loren Hauser⁸  Miriam Land⁸ 

[1] Agricultural Research Council- Agrobiology and Pedology Centre (ABP) P.za D'Azeglio, 30, 50121, Firenze, Italy;DOE Joint Genome Institute, Walnut Creek, California, USA;Department of Evolutionary Biology, University of Firenze, via Romana 17, I-50125, Firenze, Italy;Department of Evolutionary Biology, University of Firenze, via Romana 17, I-50125, Firenze, Italy;Interdisciplinary Research Institute - CNRS, Villenenuve d'Ascq, France;Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, USA;Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, 43, bvd du 11 novembre, Lyon, France;Los Alamos National Laboratory, 1619 Central Avenue, Los Alamos, USA;Oak Ridge National Laboratory, Oak Ridge, USA;

关键词: Sinorhizobium meliloti;    nodulation;    symbiosis;    comparative genomics;    pangenome;    panregulon;   

DOI  :  10.1186/1471-2164-12-235

 received in 2011-03-02, accepted in 2011-05-12,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundSinorhizobium 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.ResultsWith 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.ConclusionsIn conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.

【 授权许可】

Unknown   
© Galardini et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.