High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain
Abstract
Abstract Ensifer meliloti Mlalz-1 (INSDC = ATZD00000000 ) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of E. meliloti Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to Ensifer meliloti IAM 12611 T , Ensifer medicae A 321 T and Ensifer numidicus ORS 1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating Ensifermore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618971
- Alternate Identifier(s):
- OSTI ID: 1416926
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Name: Standards in Genomic Sciences Journal Volume: 12 Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Root-nodule bacteria; Ensifer; Geba-Rnb; Medicago; lpiA-acvB operon
Citation Formats
Osman, Wan Adnawani Meor, van Berkum, Peter, León-Barrios, Milagros, Velázquez, Encarna, Elia, Patrick, Tian, Rui, Ardley, Julie, Gollagher, Margaret, Seshadri, Rekha, Reddy, T. B. K., Ivanova, Natalia, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Baeshen, Mohamed N., Baeshen, Naseebh Nabeeh, Kyrpides, Nikos, and Reeve, Wayne. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. United Kingdom: N. p., 2017.
Web. doi:10.1186/s40793-017-0270-2.
Osman, Wan Adnawani Meor, van Berkum, Peter, León-Barrios, Milagros, Velázquez, Encarna, Elia, Patrick, Tian, Rui, Ardley, Julie, Gollagher, Margaret, Seshadri, Rekha, Reddy, T. B. K., Ivanova, Natalia, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Baeshen, Mohamed N., Baeshen, Naseebh Nabeeh, Kyrpides, Nikos, & Reeve, Wayne. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. United Kingdom. https://doi.org/10.1186/s40793-017-0270-2
Osman, Wan Adnawani Meor, van Berkum, Peter, León-Barrios, Milagros, Velázquez, Encarna, Elia, Patrick, Tian, Rui, Ardley, Julie, Gollagher, Margaret, Seshadri, Rekha, Reddy, T. B. K., Ivanova, Natalia, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Baeshen, Mohamed N., Baeshen, Naseebh Nabeeh, Kyrpides, Nikos, and Reeve, Wayne. Mon .
"High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain". United Kingdom. https://doi.org/10.1186/s40793-017-0270-2.
@article{osti_1618971,
title = {High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain},
author = {Osman, Wan Adnawani Meor and van Berkum, Peter and León-Barrios, Milagros and Velázquez, Encarna and Elia, Patrick and Tian, Rui and Ardley, Julie and Gollagher, Margaret and Seshadri, Rekha and Reddy, T. B. K. and Ivanova, Natalia and Woyke, Tanja and Pati, Amrita and Markowitz, Victor and Baeshen, Mohamed N. and Baeshen, Naseebh Nabeeh and Kyrpides, Nikos and Reeve, Wayne},
abstractNote = {Abstract Ensifer meliloti Mlalz-1 (INSDC = ATZD00000000 ) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of E. meliloti Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to Ensifer meliloti IAM 12611 T , Ensifer medicae A 321 T and Ensifer numidicus ORS 1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating Ensifer strains, but ≤93% with nodC of Ensifer strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced E. meliloti strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In E. medicae strain WSM419 , lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of E. medicae strains, which suggests genetic recombination between strain Mlalz-1 and E. medicae and the horizontal gene transfer of lpiA-acvB .},
doi = {10.1186/s40793-017-0270-2},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United Kingdom},
year = {Mon Sep 25 00:00:00 EDT 2017},
month = {Mon Sep 25 00:00:00 EDT 2017}
}
https://doi.org/10.1186/s40793-017-0270-2
Works referenced in this record:
Symbiotic characteristics of Rhizobium meliloti: and appraisal of the systematic treatment of nodulation and nitrogen fixation interactions between hosts and Rhizobia of diverse origins
journal, January 1966
- Brockwell, J.; Hely, Fw
- Australian Journal of Agricultural Research, Vol. 17, Issue 6
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015
- Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
- Standards in Genomic Sciences, Vol. 10, Issue 1
Identification and cloning of the bacterial nodulation specificity gene in the Sinorhizobium meliloti Medicago laciniata symbiosis
journal, September 2002
- Barran, L. R.; Bromfield, E. S. P.; Brown, D. C. W.
- Canadian Journal of Microbiology, Vol. 48, Issue 9
In Rhizobium meliloti, the operon associated with the nod box n5 comprises nodL, noeA and noeB, three host-range genes specifically required for the nodulation of particular Medicago species
journal, August 1995
- Ardourel, Maryvonne; Lortet, Gilles; Maillet, Fabienne
- Molecular Microbiology, Vol. 17, Issue 4
Medicago - Sinorhizobium symbiotic specificity evolution and the geographic expansion of Medicago: Medicago - Sinorhizobium evolution
journal, October 2005
- BÉNa, G.; Lyet, A.; Huguet, T.
- Journal of Evolutionary Biology, Vol. 18, Issue 6
Improving Microbial Genome Annotations in an Integrated Database Context
journal, February 2013
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- PLoS ONE, Vol. 8, Issue 2
Chromosomal and Symbiotic Relationships of Rhizobia Nodulating Medicago truncatula and M. laciniata
journal, October 2007
- van Berkum, P.; Badri, Y.; Elia, P.
- Applied and Environmental Microbiology, Vol. 73, Issue 23
Rhizobium meliloti NodP and NodQ form a multifunctional sulfate-activating complex requiring GTP for activity.
journal, November 1994
- Schwedock, J. S.; Liu, C.; Leyh, T. S.
- Journal of Bacteriology, Vol. 176, Issue 22
Rhizobium meliloti nodD genes mediate host-specific activation of nodABC.
journal, February 1990
- Honma, M. A.; Asomaning, M.; Ausubel, F. M.
- Journal of Bacteriology, Vol. 172, Issue 2
Reduction of the nodulation barrier inMedicago laciniata by alteration of the root temperature
journal, February 1981
- Jordan, D. C.
- Plant and Soil, Vol. 61, Issue 1-2
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
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
Symbiotic host-specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal
journal, April 1990
- Lerouge, Patrice; Roche, Philippe; Faucher, Catherine
- Nature, Vol. 344, Issue 6268
Secretion systems in Gram-negative bacteria: structural and mechanistic insights
journal, May 2015
- Costa, Tiago R. D.; Felisberto-Rodrigues, Catarina; Meir, Amit
- Nature Reviews Microbiology, Vol. 13, Issue 6
The type II secretion system: biogenesis, molecular architecture and mechanism
journal, April 2012
- Korotkov, Konstantin V.; Sandkvist, Maria; Hol, Wim G. J.
- Nature Reviews Microbiology, Vol. 10, Issue 5
Nitrogen-fixing sinorhizobia with Medicago laciniata constitute a novel biovar (bv. medicaginis) of S. meliloti
journal, November 2006
- Villegas, Maria Del Carmen; Rome, Sophie; Mauré, Lucette
- Systematic and Applied Microbiology, Vol. 29, Issue 7
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
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
Evidence for a Third Uptake Hydrogenase Phenotype among the Soybean Bradyrhizobia
journal, January 1990
- van Berkum, Peter
- Applied and Environmental Microbiology, Vol. 56, Issue 12
PHASTER: a better, faster version of the PHAST phage search tool
journal, May 2016
- Arndt, David; Grant, Jason R.; Marcu, Ana
- Nucleic Acids Research, Vol. 44, Issue W1
The Genomic Standards Consortium
journal, June 2011
- Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy
- PLoS Biology, Vol. 9, Issue 6
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
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
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
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.
journal, October 1994
- De Lajudie, P.; Willems, A.; Pot, B.
- International Journal of Systematic Bacteriology, Vol. 44, Issue 4
Rhizobium Lipo-Chitooligosaccharide Nodulation Factors: Signaling Molecules Mediating Recognition and Morphogenesis
journal, June 1996
- Dénarié, Jean; Debellé, Frédéric; Promé, Jean-Claude
- Annual Review of Biochemistry, Vol. 65, Issue 1
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
Microbial species delineation using whole genome sequences
journal, July 2015
- Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
- Nucleic Acids Research, Vol. 43, Issue 14
Rhizobium sp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems
journal, April 2009
- Schmeisser, C.; Liesegang, H.; Krysciak, D.
- Applied and Environmental Microbiology, Vol. 75, Issue 12
Regulation of exopolysaccharide production in Rhizobium leguminosarum biovar viciae WSM710 involves exoR
journal, June 1997
- Reeve, W. G.; Dilworth, M. J.; Tiwari, R. P.
- Microbiology, Vol. 143, Issue 6
Factors affecting the potential contributions of N2 fixation by legumes in Australian pasture systems
journal, January 2012
- Peoples, M. B.; Brockwell, J.; Hunt, J. R.
- Crop and Pasture Science, Vol. 63, Issue 9
An Essential Role for actA in Acid Tolerance of Rhizobium Melilotix
journal, March 1996
- Tiwari, R. P.; Reeve, W. G.; Dilworthan, M. J.
- Microbiology, Vol. 142, Issue 3
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model
journal, August 2007
- Jones, Kathryn M.; Kobayashi, Hajime; Davies, Bryan W.
- Nature Reviews Microbiology, Vol. 5, Issue 8
Symbiotic diversity of Ensifer meliloti strains recovered from various legume species in Tunisia
journal, December 2009
- Mnasri, Bacem; Badri, Yazid; Saïdi, Sabrine
- Systematic and Applied Microbiology, Vol. 32, Issue 8
Horizontal Gene Transfer and Homologous Recombination Drive the Evolution of the Nitrogen-Fixing Symbionts of Medicago Species
journal, May 2007
- Bailly, X.; Olivieri, I.; Brunel, B.
- Journal of Bacteriology, Vol. 189, Issue 14
Growth, photosynthesis and water relations as affected by different drought regimes and subsequent recovery in Medicago laciniata (L.) populations
journal, February 2016
- Yousfi, Nasreddine; Sihem, Ncib; Ramzi, Amari
- Journal of Plant Biology, Vol. 59, Issue 1
Sinorhizobium medicae sp. nov., Isolated from Annual Medicago spp.
journal, October 1996
- Rome, S.; Fernandez, M. P.; Brunel, B.
- International Journal of Systematic Bacteriology, Vol. 46, Issue 4
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
The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination 'Sinorhizobium adhaerens' (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion
journal, November 2003
- Young, J. M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 6
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
journal, October 2014
- Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
- Nucleic Acids Research, Vol. 43, Issue D1
Discordant Phylogenies within the rrn Loci of Rhizobia
journal, May 2003
- van Berkum, P.; Terefework, Z.; Paulin, L.
- Journal of Bacteriology, Vol. 185, Issue 10
Variation in flowering times and agronomic characteristics of Medicago laciniata (L.) Miller collected from diverse locations in New South Wales
journal, January 1992
- Young, Rr; Croft, Ph; Sandral, Ga
- Australian Journal of Experimental Agriculture, Vol. 32, Issue 1
Confidence Limits on Phylogenies: an Approach Using the Bootstrap
journal, July 1985
- Felsenstein, Joseph
- Evolution, Vol. 39, Issue 4
In vitro sulfotransferase activity of Rhizobium meliloti NodH protein: lipochitooligosaccharide nodulation signals are sulfated after synthesis of the core structure.
journal, March 1995
- Schultze, M.; Staehelin, C.; Rohrig, H.
- Proceedings of the National Academy of Sciences, Vol. 92, Issue 7
Acid tolerance in Rhizobium meliloti strain WSM419 involves a two-component sensor-regulator system
journal, July 1996
- Tiwari, R. P.; Reeve, W. G.; Dilworth, M. J.
- Microbiology, Vol. 142, Issue 7
A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey
journal, February 2015
- Reeve, Wayne; Ardley, Julie; Tian, Rui
- Standards in Genomic Sciences, Vol. 10, Issue 1
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
The transcriptional regulator gene phrR in Sinorhizobium meliloti WSM419 is regulated by low pH and other stresses
journal, December 1998
- Reeve, W. G.; Tiwari, R. P.; Wong, C. M.
- Microbiology, Vol. 144, Issue 12
Role of the Rhizobium meliloti nodF and nodE genes in the biosynthesis of lipo-oligosaccharidic nodulation factors.
journal, September 1993
- Demont, N.; Debellé, F.; Aurelle, H.
- Journal of Biological Chemistry, Vol. 268, Issue 27
Probing for pH-Regulated Genes in <i>Sinorhizobium medicae</i> Using Transcriptional Analysis
journal, January 2004
- Tiwari, Ravi P.; Reeve, Wayne G.; Fenner, Beau J.
- Journal of Molecular Microbiology and Biotechnology, Vol. 7, Issue 3
Probing for pH-Regulated Proteins in <i>Sinorhizobium medicae </i>Using Proteomic Analysis
journal, January 2004
- Reeve, Wayne G.; Tiwari, Ravi P.; Guerreiro, Nelson
- Journal of Molecular Microbiology and Biotechnology, Vol. 7, Issue 3
Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013
- Nawrocki, E. P.; Eddy, S. R.
- Bioinformatics, Vol. 29, Issue 22
Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria
journal, November 2015
- Seshadri, Rekha; Reeve, Wayne G.; Ardley, Julie K.
- Scientific Reports, Vol. 5, Issue 1
The Sinorhizobium medicae WSM419 lpiA gene is transcriptionally activated by FsrR and required to enhance survival in lethal acid conditions
journal, October 2006
- Reeve, W. G.
- Microbiology, Vol. 152, Issue 10
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013
- Tamura, Koichiro; Stecher, Glen; Peterson, Daniel
- Molecular Biology and Evolution, Vol. 30, Issue 12
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
ActP controls copper homeostasis in Rhizobium leguminosarum bv. viciae and Sinorhizobium meliloti preventing low pH-induced copper toxicity
journal, February 2002
- Reeve, Wayne G.; Tiwari, Ravi P.; Kale, Neetin B.
- Molecular Microbiology, Vol. 43, Issue 4
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.
journal, August 2009
- Merabet, C.; Martens, M.; Mahdhi, M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 3