High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland

Mazur, Andrzej; De Meyer, Sofie E.; Tian, Rui; Wielbo, Jerzy; Zebracki, Kamil; Seshadri, Rekha; Reddy, T. B.K.; Markowitz, Victor; Ivanova, Natalia N.; Pati, Amrita; Woyke, Tanja; Kyrpides, Nikos C.; Reeve, Wayne

doi:10.1186/s40793-015-0029-6

High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland

Journal Article · Thu Jul 16 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0029-6· OSTI ID:1256927

Mazur, Andrzej ^[1]; De Meyer, Sofie E. ^[2]; Tian, Rui ^[2]; Wielbo, Jerzy ^[1]; Zebracki, Kamil ^[1]; Seshadri, Rekha ^[3]; Reddy, T. B.K. ^[3]; Markowitz, Victor ^[4]; Ivanova, Natalia N. ^[3]; Pati, Amrita ^[3]; Woyke, Tanja ^[3]; Kyrpides, Nikos C. ^[5]; Reeve, Wayne ^[2]

Maria Curie-Sklodowska Univ., Lublin (Poland)
Murdoch Univ., (Western Australia)
DOE Joint Genome Inst., Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
DOE Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

We report that Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule recovered from the roots of Pisum sativum growing at Janow. GB30 is also an effective microsymbiont of the annual forage legumes vetch and pea. Here we describe the features of R. leguminosarum bv. viciae strain GB30, together with sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and 75 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; AC52-07NA27344

OSTI ID:: 1256927

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 10; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (43)

Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai Molecular Biology Reports, Vol. 47, Issue 3 https://doi.org/10.1007/s11033-020-05279-9	journal	February 2020
Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants Franche, Claudine; Lindström, Kristina; Elmerich, Claudine Plant and Soil, Vol. 321, Issue 1-2 https://doi.org/10.1007/s11104-008-9833-8	journal	December 2008
Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? Masson-Boivin, Catherine; Giraud, Eric; Perret, Xavier Trends in Microbiology, Vol. 17, Issue 10 https://doi.org/10.1016/j.tim.2009.07.004	journal	October 2009
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
PICRUSt2 for prediction of metagenome functions Douglas, Gavin M.; Maffei, Vincent J.; Zaneveld, Jesse R. Nature Biotechnology, Vol. 38, Issue 6 https://doi.org/10.1038/s41587-020-0548-6	journal	June 2020
High-quality draft assemblies of mammalian genomes from massively parallel sequence data Gnerre, S.; MacCallum, I.; Przybylski, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 4 https://doi.org/10.1073/pnas.1017351108	journal	December 2010
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Pruesse, E.; Quast, C.; Knittel, K. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm864	journal	November 2007
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata Pagani, I.; Liolios, K.; Jansson, J. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1100	journal	December 2011
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
Approved Lists of Bacterial Names Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D. International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1 https://doi.org/10.1099/00207713-30-1-225	journal	January 1980
Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris Nodules Amarger, N.; Macheret, V.; Laguerre, G. International Journal of Systematic Bacteriology, Vol. 47, Issue 4 https://doi.org/10.1099/00207713-47-4-996	journal	October 1997
Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Young, J. M. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 3 https://doi.org/10.1099/00207713-51-3-945	journal	May 2001
R Factor Transfer in Rhizobium leguminosarum Beringer, J. E. Microbiology, Vol. 84, Issue 1 https://doi.org/10.1099/00221287-84-1-188	journal	September 1974
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species Kim, O. -S.; Cho, Y. -J.; Lee, K. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 3 https://doi.org/10.1099/ijs.0.038075-0	journal	November 2011
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. Ramirez-Bahena, M. H.; Garcia-Fraile, P.; Peix, A. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 11 https://doi.org/10.1099/ijs.0.65621-0	journal	November 2008
Genetic and Metabolic Divergence within a Rhizobium leguminosarum bv. trifolii Population Recovered from Clover Nodules Wielbo, Jerzy; Marek-Kozaczuk, Monika; Mazur, Andrzej Applied and Environmental Microbiology, Vol. 76, Issue 14 https://doi.org/10.1128/aem.00667-10	journal	May 2010
Intragenomic diversity of Rhizobium leguminosarum bv. trifolii clover nodule isolates Mazur, Andrzej; Stasiak, Grażyna; Wielbo, Jerzy BMC Microbiology, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2180-11-123	journal	January 2011
A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey Reeve, Wayne; Ardley, Julie; Tian, Rui Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/1944-3277-10-14	journal	February 2015
Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum. Reeve, Wayne; O’Hara, Graham; Chain, Patrick Standards in Genomic Sciences, Vol. 2, Issue 1 https://doi.org/10.4056/sigs.44642	journal	February 2010
Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum Terpolilli, Jason; Rui, Tian; Yates, Ron Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.4988693	journal	December 2013
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.632	journal	July 2009
Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers. Reeve, Wayne; O’Hara, Graham; Chain, Patrick Standards in Genomic Sciences, Vol. 2, Issue 3 https://doi.org/10.4056/sigs.852027	journal	June 2010
The Structure and Metabolic Diversity of Population of Pea Microsymbionts Isolated from Root Nodules Wielbo, Jerzy British Microbiology Research Journal, Vol. 1, Issue 3 https://doi.org/10.9734/bmrj/2011/412	journal	January 2011
Selection for acid tolerance inRhizobium meliloti Howieson, J. G.; Ewing, M. A.; D'Antuono, M. F. Plant and Soil, Vol. 105, Issue 2 https://doi.org/10.1007/BF02376781	journal	September 1988
Optimising the legume symbiosis in stressful and competitive environments within southern Australia?some contemporary thoughts Howieson, J. Soil Biology and Biochemistry, Vol. 36, Issue 8 https://doi.org/10.1016/j.soilbio.2004.04.008	journal	August 2004
Symbiovars in rhizobia reflect bacterial adaptation to legumes Rogel, Marco A.; Ormeño-Orrillo, Ernesto; Martinez Romero, Esperanza Systematic and Applied Microbiology, Vol. 34, Issue 2 https://doi.org/10.1016/j.syapm.2010.11.015	journal	April 2011
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Tamura, K.; Peterson, D.; Peterson, N. Molecular Biology and Evolution, Vol. 28, Issue 10 https://doi.org/10.1093/molbev/msr121	journal	May 2011
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum Kumar, Nitin; Lad, Ganesh; Giuntini, Elisa Open Biology, Vol. 5, Issue 1 https://doi.org/10.1098/rsob.140133	journal	January 2015
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. Kuykendall, L. D.; Kerr, A.; Young, J. M. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 1 https://doi.org/10.1099/00207713-51-1-89	journal	January 2001
Rhizobium laguerreae sp. nov. nodulates Vicia faba on several continents Saïdi, Sabrine; Ramírez-Bahena, Martha-Helena; Santillana, Nery International Journal of Systematic and Evolutionary Microbiology, Vol. 64, Issue Pt_1 https://doi.org/10.1099/ijs.0.052191-0	journal	January 2014
Validation of publication of new names and new combinations previously effectively published outside the IJSEM Euzeby, Jean International Journal of Systematic and Evolutionary Microbiology, Vol. 55, Issue 6, p. 2235-2238 https://doi.org/10.1099/ijs.0.64108-0	journal	November 2005
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Genetic and Metabolic Divergence within a Rhizobium leguminosarum bv. trifolii Population Recovered from Clover Nodules Wielbo, Jerzy; Marek-Kozaczuk, Monika; Mazur, Andrzej Applied and Environmental Microbiology, Vol. 76, Issue 14 https://doi.org/10.1128/AEM.00667-10	journal	May 2010
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
The genome of Rhizobium leguminosarum has recognizable core and accessory components Young, J. Peter W.; Crossman, Lisa C.; Johnston, Andrew W. B. Genome Biology, Vol. 7, Issue 4, p. R34 https://doi.org/10.1186/gb-2006-7-4-r34	journal	April 2006
The Genomic Standards Consortium Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy PLoS Biology, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pbio.1001088	journal	June 2011
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S. PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0048837	journal	December 2012
Improving Microbial Genome Annotations in an Integrated Database Context Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0054859	journal	February 2013
The Structure and Metabolic Diversity of Population of Pea Microsymbionts Isolated from Root Nodules Wielbo, Jerzy British Microbiology Research Journal, Vol. 1, Issue 3 https://doi.org/10.9734/BMRJ/2011/412	journal	January 2011

Cited By (2)

Electrophoretic profiles of lipopolysaccharides from Rhizobium strains nodulating Pisum sativum do not reflect phylogenetic relationships between these strains Kutkowska, Jolanta; Marek-Kozaczuk, Monika; Wielbo, Jerzy Archives of Microbiology, Vol. 199, Issue 7 https://doi.org/10.1007/s00203-017-1374-1	journal	April 2017
Structural and functional organization of the plasmid regulons of Rhizobium leguminosarum symbiotic genes Chirak, E. R.; Kopat’, V. V.; Kimeklis, A. K. Microbiology, Vol. 85, Issue 6 https://doi.org/10.1134/s0026261716060072	journal	November 2016

Similar Records

Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers.

Journal Article · Thu Dec 31 23:00:00 EST 2009 · Standards in Genomic Sciences · OSTI ID:1043958

Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565.

Journal Article · Sat Dec 14 23:00:00 EST 2013 · Standards in Genomic Sciences · OSTI ID:1628671

Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.

Journal Article · Sat Dec 14 23:00:00 EST 2013 · Standards in Genomic Sciences · OSTI ID:1628672

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Alphaproteobacteria
GEBA-RNB
Nitrogen fixation
Rhizobia
Root-nodule bacteria

High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland

Citation Formats

References (43)

Cited By (2)

Similar Records

Related Subjects