Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A

Simon Kelly,Nikos Kyrpides,Wayne Reeve,Natalia Ivanova,Victor Markowitz,Lambert Bräu,Tanja Woyke,John Sullivan,Christine Munk,Rui Tian,Tatiparthi Reddy,Amrita Pati,Clive Ronson,Lynne Goodwin,Cliff Han,Marcel Huntemann,Konstantinos Mavromatis

doi:10.1186/1944-3277-9-6

Abstract

Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a Lotus corniculatus root nodule and is a reisolate of the inoculant strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative, non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or ICEMlSymR7A. M. loti is the microsymbiont of the model legume Lotus japonicus and strain R7A has been used extensively in studies of the plant-microbe interaction. This report reveals that the genome of M. loti strain R7A does not harbor any plasmids and contains a single scaffold of size 6,529,530 bp which encodes 6,323 protein-coding genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Highlights

Mesorhizobium loti strain R7A is a reisolate of strain ICMP3513 (International Culture Collection of Microorganisms from Plants, LandCare Research, Auckland, New Zealand)
It was isolated from a root nodule taken from a stand of Lotus corniculatus in Lammermoor, Central Otago, New Zealand, inoculated seven years earlier with strain ICMP3153 [1]
Strain R7A contains a 502-kb symbiosis island, known as ICEMlSymR7A, that was discovered through its ability to transfer from strain ICMP3153 to indigenous nonsymbiotic mesorhizobia at the Lammermoor field site [1,3]

Summary

Introduction

Mesorhizobium loti strain R7A is a reisolate of strain ICMP3513 (International Culture Collection of Microorganisms from Plants, LandCare Research, Auckland, New Zealand). A nonsymbiotic derivative of R7A cured of the symbiosis island and unable to form root nodules has been isolated and is called R7ANS [5] Genome project history This organism was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the Community Sequencing Program at the U.S Department of Energy, Joint Genome Institute (JGI) for projects of relevance to agency missions. Genome sequencing and assembly The draft genome of M. loti R7A was generated at the DOE Joint Genome Institute (JGI) using Illumina data [32]. The Illumina draft data were assembled with Velvet, version 1.1.05 [34], and the consensus sequences were computationally shredded into 1.5 Kbp overlapping fake reads (shreds).

1.56 Nucleotide transport and metabolism

Findings

Conclusions