Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.
Abstract
Rhizobium leguminosarum bv. trifolii SRDI943 (strain syn. V2-2) is an aerobic, motile, Gramnegative, non-spore-forming rod that was isolated from a root nodule of Trifolium michelianum Savi cv. Paradana that had been grown in soil collected from a mixed pasture in Victoria, Australia. This isolate was found to have a broad clover host range but was sub-optimal for nitrogen fixation with T. subterraneum (fixing 20-54% of reference inoculant strain WSM1325) and was found to be totally ineffective with the clover species T. polymorphum and T. pratense. Here we describe the features of R. leguminosarum bv. trifolii strain SRDI943, together with genome sequence information and annotation. The 7,412,387 bp high-quality-draft genome is arranged into 5 scaffolds of 5 contigs, contains 7,317 protein-coding genes and 89 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
- Authors:
-
- Murdoch Univ., WA (Australia). Centre for Rhizobium Studies
- South Australian Research and Development Inst., Urrbrae (Australia)
- Deakin Univ., Melbourne, VIC (Australia). Faculty of Science and Technology. School of Life and Environmental Sciences
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Biosciences Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Biosciences Division
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1628672
- Grant/Contract Number:
- AC52-06NA25396; AC02-05CH11231; AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 2; Journal ID: ISSN 1944-3277
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Microbiology
Citation Formats
Reeve, Wayne, Drew, Elizabeth, Ballard, Ross, Melino, Vanessa, Tian, Rui, De Meyer, Sofie, Brau, Lambert, Ninawi, Mohamed, Daligault, Hajnalka, Davenport, Karen, Erkkila, Tracy, Goodwin, Lynne, Gu, Wei, Munk, Christine, Teshima, Hazuki, Xu, Yan, Chain, Patrick, and Kyrpides, Nikos. Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.. United States: N. p., 2013.
Web. doi:10.4056/sigs.4478252.
Reeve, Wayne, Drew, Elizabeth, Ballard, Ross, Melino, Vanessa, Tian, Rui, De Meyer, Sofie, Brau, Lambert, Ninawi, Mohamed, Daligault, Hajnalka, Davenport, Karen, Erkkila, Tracy, Goodwin, Lynne, Gu, Wei, Munk, Christine, Teshima, Hazuki, Xu, Yan, Chain, Patrick, & Kyrpides, Nikos. Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.. United States. https://doi.org/10.4056/sigs.4478252
Reeve, Wayne, Drew, Elizabeth, Ballard, Ross, Melino, Vanessa, Tian, Rui, De Meyer, Sofie, Brau, Lambert, Ninawi, Mohamed, Daligault, Hajnalka, Davenport, Karen, Erkkila, Tracy, Goodwin, Lynne, Gu, Wei, Munk, Christine, Teshima, Hazuki, Xu, Yan, Chain, Patrick, and Kyrpides, Nikos. Sun .
"Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.". United States. https://doi.org/10.4056/sigs.4478252. https://www.osti.gov/servlets/purl/1628672.
@article{osti_1628672,
title = {Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.},
author = {Reeve, Wayne and Drew, Elizabeth and Ballard, Ross and Melino, Vanessa and Tian, Rui and De Meyer, Sofie and Brau, Lambert and Ninawi, Mohamed and Daligault, Hajnalka and Davenport, Karen and Erkkila, Tracy and Goodwin, Lynne and Gu, Wei and Munk, Christine and Teshima, Hazuki and Xu, Yan and Chain, Patrick and Kyrpides, Nikos},
abstractNote = {Rhizobium leguminosarum bv. trifolii SRDI943 (strain syn. V2-2) is an aerobic, motile, Gramnegative, non-spore-forming rod that was isolated from a root nodule of Trifolium michelianum Savi cv. Paradana that had been grown in soil collected from a mixed pasture in Victoria, Australia. This isolate was found to have a broad clover host range but was sub-optimal for nitrogen fixation with T. subterraneum (fixing 20-54% of reference inoculant strain WSM1325) and was found to be totally ineffective with the clover species T. polymorphum and T. pratense. Here we describe the features of R. leguminosarum bv. trifolii strain SRDI943, together with genome sequence information and annotation. The 7,412,387 bp high-quality-draft genome is arranged into 5 scaffolds of 5 contigs, contains 7,317 protein-coding genes and 89 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.},
doi = {10.4056/sigs.4478252},
journal = {Standards in Genomic Sciences},
number = 2,
volume = 9,
place = {United States},
year = {Sun Dec 15 00:00:00 EST 2013},
month = {Sun Dec 15 00:00:00 EST 2013}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The Chemistry and Agronomic Effectiveness of Phosphate Fertilizers
journal, November 1998
- Bolland, Mike D. A.; Gilkes, Robert J.
- Journal of Crop Production, Vol. 1, Issue 2
Global inputs of biological nitrogen fixation in agricultural systems
journal, July 2008
- Herridge, David F.; Peoples, Mark B.; Boddey, Robert M.
- Plant and Soil, Vol. 311, Issue 1-2
Prospects and problems of simple linear models for estimating symbiotic N2 fixation by crop and pasture legumes
journal, August 2009
- Unkovich, M. J.; Baldock, J.; Peoples, M. B.
- Plant and Soil, Vol. 329, Issue 1-2
Distribution, abundance and symbiotic effectiveness of Rhizobium leguminosarum bv. trifolii from alkaline pasture soils in South Australia
journal, January 2000
- Denton, M. D.; Coventry, D. R.; Bellotti, W. D.
- Australian Journal of Experimental Agriculture, Vol. 40, Issue 1
Symbiotic performance of Mediterranean Trifolium spp. with naturalised soil rhizobia
journal, January 2011
- Drew, E. A.; Charman, N.; Dingemanse, R.
- Crop and Pasture Science, Vol. 62, Issue 10
Effectiveness of Rhizobium trifolii populations associated with Trifolium species in Taranaki, New Zealand
journal, July 1981
- Rys, G. J.; Bonish, P. M.
- New Zealand Journal of Experimental Agriculture, Vol. 9, Issue 3-4
Improving N2 fixation from the plant down: Compatibility of Trifolium subterraneum L. cultivars with soil rhizobia can influence symbiotic performance
journal, June 2009
- Drew, E. A.; Ballard, R. A.
- Plant and Soil, Vol. 327, Issue 1-2
Identifying abnormalities in symbiotic development between Trifolium spp. and Rhizobium leguminosarum bv. trifolii leading to sub-optimal and ineffective nodule phenotypes
journal, September 2012
- Melino, V. J.; Drew, E. A.; Ballard, R. A.
- Annals of Botany, Vol. 110, Issue 8
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
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
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
Approved Lists of Bacterial Names
journal, January 1980
- Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1
A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis.
journal, January 2001
- Kuykendall, L. D.; Kerr, A.; Young, J. M.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 1
Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov.
journal, November 2008
- Ramirez-Bahena, M. H.; Garcia-Fraile, P.; Peix, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 11
OPINION 34: Conservation of the Generic Name Rhizobium Frank 1889
journal, January 1970
- Editorial Secretary (for the Judicial Commission of the International Committee on Nomenclature of Bacteria),
- International Journal of Systematic Bacteriology, Vol. 20, Issue 1, p. 11-12
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
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
Confidence Limits on Phylogenies: An Approach Using the Bootstrap
journal, July 1985
- Felsenstein, Joseph
- Evolution, Vol. 39, Issue 4, p. 783-791
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
Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria
journal, June 1999
- Reeve, W. G.; Tiwari, R. P.; Worsley, P. S.
- Microbiology, Vol. 145, Issue 6
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998
- Ewing, Brent; Green, Phil
- Genome Research, Vol. 8, Issue 3
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
journal, March 1998
- Ewing, Brent; Hillier, LaDeana; Wendl, Michael C.
- Genome Research, Vol. 8, Issue 3
Consed: A Graphical Tool for Sequence Finishing
journal, March 1998
- Gordon, David; Abajian, Chris; Green, Phil
- Genome Research, Vol. 8, Issue 3
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
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
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007
- Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas
- Nucleic Acids Research, Vol. 35, Issue 9
Rfam: an RNA family database
journal, January 2003
- Griffiths-Jones, S.
- Nucleic Acids Research, Vol. 31, Issue 1
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001
- Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 305, Issue 3
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass
journal, February 2020
- Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai
- Molecular Biology Reports, Vol. 47, Issue 3
Genetic diversity of Amomum xanthioides and its related species from Southeast Asia and China
journal, May 2021
- Sone, Mikako; Zhu, Shu; Cheng, Xiao
- Journal of Natural Medicines, Vol. 75, Issue 4
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
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
Dietary palmitic acid promotes a prometastatic memory via Schwann cells
journal, November 2021
- Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc
- Nature, Vol. 599, Issue 7885
Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing
journal, July 2020
- Brofelth, Mattias; Ekstrand, Anna Isinger; Gour, Shashank
- Communications Biology, Vol. 3, Issue 1
Effectiveness of Rhizobium trifolii populations associated with Trifolium species in Taranaki, New Zealand
journal, July 1981
- Rys, G. J.; Bonish, P. M.
- New Zealand Journal of Experimental Agriculture, Vol. 9, Issue 3-4
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
Rfam: an RNA family database
journal, January 2003
- Griffiths-Jones, S.
- Nucleic Acids Research, Vol. 31, Issue 1
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007
- Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas
- Nucleic Acids Research, Vol. 35, Issue 9
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
Approved Lists of Bacterial Names
journal, January 1980
- Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1
Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria
journal, June 1999
- Reeve, W. G.; Tiwari, R. P.; Worsley, P. S.
- Microbiology, Vol. 145, Issue 6
Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov.
journal, November 2008
- Ramirez-Bahena, M. H.; Garcia-Fraile, P.; Peix, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 11
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
Works referencing / citing this record:
Measurements of carbon utilization by single bacterial species in sterile soil: insights into Rhizobium spp.
journal, June 2016
- Wigley, K.; Wakelin, S. A.; Moot, D. J.
- Journal of Applied Microbiology, Vol. 121, Issue 2