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Title: High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

Abstract

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml SymR7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds of 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

Authors:
 [1];  [2];  [2];  [1];  [3];  [3];  [4];  [4];  [4];  [4];  [5];  [4];  [6]
  1. Murdoch Univ. Perth, WA (Australia). Centre for Rhizobium Studies
  2. Univ. of Otago, Dunedin (New Zealand)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. DOE Joint Genome Institute, Walnut Creek, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1255535
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Root-nodule bacteria; Nitrogen fixation; Symbiosis; Alphaproteobacteria; GEBA-RNB

Citation Formats

Reeve, Wayne, Sullivan, John, Ronson, Clive, Tian, Rui, Munk, Christine, Han, Cliff, Reddy, T. B. K., Seshadri, Rekha, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Ivanova, Natalia, and Kyrpides, Nikos. High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0049-2.
Reeve, Wayne, Sullivan, John, Ronson, Clive, Tian, Rui, Munk, Christine, Han, Cliff, Reddy, T. B. K., Seshadri, Rekha, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Ivanova, Natalia, & Kyrpides, Nikos. High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym. United States. doi:10.1186/s40793-015-0049-2.
Reeve, Wayne, Sullivan, John, Ronson, Clive, Tian, Rui, Munk, Christine, Han, Cliff, Reddy, T. B. K., Seshadri, Rekha, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Ivanova, Natalia, and Kyrpides, Nikos. Fri . "High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym". United States. doi:10.1186/s40793-015-0049-2. https://www.osti.gov/servlets/purl/1255535.
@article{osti_1255535,
title = {High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym},
author = {Reeve, Wayne and Sullivan, John and Ronson, Clive and Tian, Rui and Munk, Christine and Han, Cliff and Reddy, T. B. K. and Seshadri, Rekha and Woyke, Tanja and Pati, Amrita and Markowitz, Victor and Ivanova, Natalia and Kyrpides, Nikos},
abstractNote = {Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml SymR7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds of 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.},
doi = {10.1186/s40793-015-0049-2},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {2015},
month = {8}
}

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Works referenced in this record:

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
journal, December 2007

  • Liolios, K.; Mavromatis, K.; Tavernarakis, N.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm884

Confidence Limits on Phylogenies: An Approach Using the Bootstrap
journal, July 1985

  • Felsenstein, Joseph
  • Evolution, Vol. 39, Issue 4, p. 783-791
  • DOI: 10.2307/2408678

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment.
journal, September 1995

  • Sullivan, J. T.; Patrick, H. N.; Lowther, W. L.
  • Proceedings of the National Academy of Sciences, Vol. 92, Issue 19
  • DOI: 10.1073/pnas.92.19.8985

Selection for acid tolerance inRhizobium meliloti
journal, September 1988

  • Howieson, J. G.; Ewing, M. A.; D'Antuono, M. F.
  • Plant and Soil, Vol. 105, Issue 2
  • DOI: 10.1007/BF02376781

Rhizobium loti, a New Species of Legume Root Nodule Bacteria
journal, July 1982

  • Jarvis, B. D. W.; Pankhurst, C. E.; Patel, J. J.
  • International Journal of Systematic Bacteriology, Vol. 32, Issue 3
  • DOI: 10.1099/00207713-32-3-378

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011

  • Tamura, K.; Peterson, D.; Peterson, N.
  • Molecular Biology and Evolution, Vol. 28, Issue 10
  • DOI: 10.1093/molbev/msr121

Solexa Ltd
journal, June 2004


The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Comparative Sequence Analysis of the Symbiosis Island of Mesorhizobium loti Strain R7A
journal, June 2002


Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene
journal, April 1998

  • Sullivan, J. T.; Ronson, C. W.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 9
  • DOI: 10.1073/pnas.95.9.5145

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011

  • Pagani, I.; Liolios, K.; Jansson, J.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1100

R Factor Transfer in Rhizobium leguminosarum
journal, September 1974


The Genomic Standards Consortium
journal, June 2011


Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System
journal, March 2000

  • Tighe, S. W.; de Lajudie, P.; Dipietro, K.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 2
  • DOI: 10.1099/00207713-50-2-787

Rhizobium meliloti ntrA (rpoN) gene is required for diverse metabolic functions.
journal, June 1987


IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012


IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009


GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

  • Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1457