High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris

Mhamdi, Ridha; Ardley, Julie; Tian, Rui; Seshadri, Rekha; Reddy, T. B. K.; Pati, Amrita; Woyke, Tanja; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

doi:10.1186/s40793-015-0005-1

Title: High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris

Journal Article · Thu Jul 02 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0005-1· OSTI ID:1256908

Mhamdi, Ridha ^[1]; Ardley, Julie ^[2]; Tian, Rui ^[2]; Seshadri, Rekha ^[3]; Reddy, T. B. K. ^[3]; Pati, Amrita ^[3]; Woyke, Tanja ^[3]; Markowitz, Victor ^[4]; Ivanova, Natalia ^[3]; Kyrpides, Nikos ^[5]; Reeve, Wayne ^[2]

Centre of Biotechnology of Borj-Cedria, Hammam-Lif (Tunisia)
Murdoch Univ., Western Australia (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 Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350 protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.

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

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

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1256908

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

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 5 works

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References (49)

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
Salt-tolerant rhizobia isolated from a Tunisian oasis that are highly effective for symbiotic N2-fixation with Phaseolus vulgaris constitute a novel biovar (bv. mediterranense) of Sinorhizobium meliloti Mnasri, Bacem; Mrabet, Moncef; Laguerre, Gisèle Archives of Microbiology, Vol. 187, Issue 1 https://doi.org/10.1007/s00203-006-0173-x	journal	September 2006
Genetic diversity of Amomum xanthioides and its related species from Southeast Asia and China Sone, Mikako; Zhu, Shu; Cheng, Xiao Journal of Natural Medicines, Vol. 75, Issue 4 https://doi.org/10.1007/s11418-021-01512-2	journal	May 2021
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
Advances in Rhizobium Research Sessitsch, A.; Howieson, J. G.; Perret, X. Critical Reviews in Plant Sciences, Vol. 21, Issue 4 https://doi.org/10.1080/0735-260291044278	journal	July 2002
Rhizobia from Lanzarote, the Canary Islands, That Nodulate Phaseolus vulgaris Have Characteristics in Common with Sinorhizobium meliloti Isolates from Mainland Spain Zurdo-Piñeiro, José Luis; García-Fraile, Paula; Rivas, Raúl Applied and Environmental Microbiology, Vol. 75, Issue 8 https://doi.org/10.1128/aem.02811-08	journal	April 2009
Characterization of root-nodulating bacteria associated to Prosopis farcta growing in the arid regions of Tunisia Fterich, A.; Mahdhi, M.; Caviedes, M. A. Archives of Microbiology, Vol. 193, Issue 6 https://doi.org/10.1007/s00203-011-0683-z	journal	February 2011
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
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
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
Multilocus sequence analysis of Brazilian Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.) reveals unexpected taxonomic diversity Ribeiro, Renan Augusto; Barcellos, Fernando Gomes; Thompson, Fabiano L. Research in Microbiology, Vol. 160, Issue 4 https://doi.org/10.1016/j.resmic.2009.03.009	journal	May 2009
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
Nodulation and growth of common bean (Phaseolus vulgaris) under water deficiency Mnasri, Bacem; Aouani, Mohamed Elarbi; Mhamdi, Ridha Soil Biology and Biochemistry, Vol. 39, Issue 7 https://doi.org/10.1016/j.soilbio.2007.01.030	journal	July 2007
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
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
Solexa Ltd Bennett, Simon Pharmacogenomics, Vol. 5, Issue 4 https://doi.org/10.1517/14622416.5.4.433	journal	June 2004
Polyphasic Taxonomy of Rhizobia: Emendation of the Genus Sinorhizobium and Description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov. De Lajudie, P.; Willems, A.; Pot, B. International Journal of Systematic Bacteriology, Vol. 44, Issue 4 https://doi.org/10.1099/00207713-44-4-715	journal	October 1994
Potential for inoculation of common bean by effective rhizobia in Tunisian soils Aouani, M. E.; Mhamdi, R.; Mars, M. Agronomie, Vol. 17, Issue 9-10 https://doi.org/10.1051/agro:19970902	journal	January 1997
Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov. Merabet, C.; Martens, M.; Mahdhi, M. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 3 https://doi.org/10.1099/ijs.0.012088-0	journal	August 2009
Symbiotic diversity of Ensifer meliloti strains recovered from various legume species in Tunisia Mnasri, Bacem; Badri, Yazid; Saïdi, Sabrine Systematic and Applied Microbiology, Vol. 32, Issue 8 https://doi.org/10.1016/j.syapm.2009.07.007	journal	December 2009
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
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
Influence of the Size of Indigenous Rhizobial Populations on Establishment and Symbiotic Performance of Introduced Rhizobia on Field-Grown Legumes Thies, Janice E.; Singleton, Paul W.; Bohlool, B. Ben Applied and Environmental Microbiology, Vol. 57, Issue 1 https://doi.org/10.1128/aem.57.1.19-28.1991	journal	January 1991
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
Phylogenetic position and revised classification ofAcacia s.l.(Fabaceae: Mimosoideae) in Africa, including new combinations inVachelliaandSenegalia Kyalangalilwa, Bruce; Boatwright, James S.; Daru, Barnabas H. Botanical Journal of the Linnean Society, Vol. 172, Issue 4 https://doi.org/10.1111/boj.12047	journal	May 2013
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
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku950	journal	October 2014
Genotypic diversity and symbiotic effectiveness of rhizobia isolated from root nodules of Phaseolus vulgaris L. grown in Tunisian soils Mhamdi, R.; Jebara, M.; Aouani, M. E. Biology and Fertility of Soils, Vol. 28, Issue 3 https://doi.org/10.1007/s003740050499	journal	January 1999
Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.) Ormeño-Orrillo, Ernesto; Menna, Pâmela; Almeida, Luiz Gonzaga P. BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-735	journal	January 2012
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
Sinorhizobium americanum symbiovar mediterranense is a predominant symbiont that nodulates and fixes nitrogen with common bean (Phaseolus vulgaris L.) in a Northern Tunisian field Mnasri, Bacem; Saïdi, Sabrine; Chihaoui, Saif-Allah Systematic and Applied Microbiology, Vol. 35, Issue 4 https://doi.org/10.1016/j.syapm.2012.04.003	journal	June 2012
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
Methods for enhancing symbiotic nitrogen fixation Hardarson, Gudni Plant and Soil, Vol. 152, Issue 1 https://doi.org/10.1007/BF00016329	journal	January 1993
Promiscuous nodulation of Phaseolus vulgaris, Macroptilium atropurpureum, and Leucaena leucocephala by indigenous Rhizobium meliloti Bromfield, E. S. P.; Barran, L. R. Canadian Journal of Microbiology, Vol. 36, Issue 5 https://doi.org/10.1139/m90-065	journal	May 1990
Nodule morphology, symbiotic specificity and association with unusual rhizobia are distinguishing features of the genus Listia within the southern African crotalarioid clade Lotononis s.l. Ardley, Julie K.; Reeve, Wayne G.; O'Hara, Graham W. Annals of Botany, Vol. 112, Issue 1 https://doi.org/10.1093/aob/mct095	journal	May 2013
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
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
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
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
Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria Reeve, W. G.; Tiwari, R. P.; Worsley, P. S. Microbiology, Vol. 145, Issue 6 https://doi.org/10.1099/13500872-145-6-1307	journal	June 1999
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
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
Draft Genome Sequence of the Bean-Nodulating Sinorhizobium fredii Strain GR64 Torres Tejerizo, Gonzalo; Lozano, Luis; González, Víctor Journal of Bacteriology, Vol. 194, Issue 24 https://doi.org/10.1128/JB.01882-12	journal	December 2012
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
Confidence Limits on Phylogenies: An Approach Using the Bootstrap Felsenstein, Joseph Evolution, Vol. 39, Issue 4, p. 783-791 https://doi.org/10.2307/2408678	journal	July 1985
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
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
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
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000

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Title: High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris

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