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Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

Masayuki Sugawara1, Brendan Epstein12, Brian D Badgley1, Tatsuya Unno1, Lei Xu1, Jennifer Reese12, Prasad Gyaneshwar3, Roxanne Denny2, Joann Mudge4, Arvind K Bharti4, Andrew D Farmer4, Gregory D May4, Jimmy E Woodward4, Claudine Médigue5, David Vallenet5, Aurélie Lajus5, Zoé Rouy5, Betsy Martinez-Vaz6, Peter Tiffin2, Nevin D Young27 and Michael J Sadowsky18*

Author Affiliations

1 BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, University of Minnesota, St Paul, MN 55108, USA

2 Department of Plant Biology, 250 Biological Sciences, 1445 Gortner Ave, University of Minnesota, St Paul, MN 55108, USA

3 Department of Biological Sciences, 3209 N. Maryland Ave, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA

4 National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA

5 CNRS, UMR8030 & UEVE, Université d'Evry & CEA/DSV/IG/Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Centre National de Séquençage, 2 rue Gaston Crémieux CP5706 91057, Evry cedex, France

6 Department of Biology, MS-B1807, 1536 Hewitt Avenue, Hamline University, St Paul, MN 55104, USA

7 Department of Plant Pathology, 495 Borlaug Hall, 1991 Upper Buford Circle, University of Minnesota, St Paul, MN 55108, USA

8 Department of Soil, Water, & Climate, 491 Borlaug Hall, 1991 Upper Buford Circle, University of Minnesota, St Paul, MN 55108, USA

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Genome Biology 2013, 14:R17  doi:10.1186/gb-2013-14-2-r17

Published: 20 February 2013

Abstract

Background

The sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group.

Results

Here we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content, including those involved in conjugation and organic sulfur utilization. Genes involved in Nod factor and polysaccharide biosynthesis, denitrification and type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency.

Conclusions

Our results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. 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.