High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

De Meyer, Sofie E.; Parker, Matthew; Van Berkum, Peter; Tian, Rui; Seshadri, Rekha; Reddy, T. B. K.; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Woyke, Tanja; Kyrpides, Nikos; Howieson, John; Reeve, Wayne

doi:10.1186/s40793-015-0074-1

Title: High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

Journal Article · Fri Oct 16 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0074-1· OSTI ID:1256939

De Meyer, Sofie E. ^[1]; Parker, Matthew ^[2]; Van Berkum, Peter ^[3]; Tian, Rui ^[1]; Seshadri, Rekha ^[4]; Reddy, T. B. K. ^[4]; Markowitz, Victor ^[5]; Ivanova, Natalia ^[4]; Pati, Amrita ^[4]; Woyke, Tanja ^[4]; Kyrpides, Nikos ^[4]; Howieson, John ^[1]; Reeve, Wayne ^[1]

Murdoch Univ. (Western Australia)
Binghamton Univ., NY (United States)
BARC-West USDA ARS, Beltsville, MD (United States)
DOE Joint Genome Inst., Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Â© 2015 De Meyer et al. Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Moreover, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Therefore, the genome of Cupriavidus sp. strain AMP6 enables comparative analyses of symbiotic trait evolution in this genus and here we describe the general features, together with sequence and annotation. The 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

View Accepted Manuscript (DOE)

Cite

Export

Save

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; AC52-07NA27344; AC02-06NA25396

OSTI ID:: 1256939

Alternate ID(s):: OSTI ID: 1378595

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

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (42)

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
Nodule Symbiosis of Invasive Mimosa pigra in Australia and in Ancestral Habitats: A Comparative Analysis Parker, Matthew A.; Wurtz, Anna K.; Paynter, Quentin Biological Invasions, Vol. 9, Issue 2 https://doi.org/10.1007/s10530-006-0009-2	journal	April 2006
Burkholderia spp. are the most competitive symbionts of Mimosa , particularly under N-limited conditions Elliott, Geoffrey N.; Chou, Jui-Hsing; Chen, Wen-Ming Environmental Microbiology, Vol. 11, Issue 4 https://doi.org/10.1111/j.1462-2920.2008.01799.x	journal	April 2009
American origin of Cupriavidus bacteria associated with invasive Mimosa legumes in the Philippines Andrus, Alexis D.; Andam, Cheryl; Parker, Matthew A. FEMS Microbiology Ecology, Vol. 80, Issue 3 https://doi.org/10.1111/j.1574-6941.2012.01342.x	journal	March 2012
Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient Chen, W. M.; Laevens, S.; Lee, T. M. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 51, Issue 5 https://doi.org/10.1099/00207713-51-5-1729	journal	September 2001
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
Phylogeny based on 16S rDNA and nifH sequences of Ralstonia taiwanensis strains isolated from nitrogen-fixing nodules of Mimosa pudica , in India Verma, Subhash Chandra; Chowdhury, Soumitra Paul; Tripathi, Anil Kumar Canadian Journal of Microbiology, Vol. 50, Issue 5 https://doi.org/10.1139/w04-020	journal	May 2004
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
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
Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia Walker, Robert; Watkin, Elizabeth; Tian, Rui Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.5008793	journal	December 2013
Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils Estrada-de los Santos, Paulina; Martínez-Aguilar, Lourdes; López-Lara, Isabel M. Systematic and Applied Microbiology, Vol. 35, Issue 5 https://doi.org/10.1016/j.syapm.2012.05.005	journal	July 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
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
Physiological and symbiotic diversity of Cupriavidus necator strains isolated from nodules of Leguminosae species Florentino, Ligiane Aparecida; Jaramillo, Paula Marcela Duque; Silva, Karina Barroso Scientia Agricola, Vol. 69, Issue 4 https://doi.org/10.1590/S0103-90162012000400003	journal	January 2012
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
Genetic diversity of Mimosa pudica rhizobial symbionts in soils of French Guiana: investigating the origin and diversity of Burkholderia phymatum and other beta-rhizobia Mishra, Ravi P. N.; Tisseyre, Pierre; Melkonian, Rémy FEMS Microbiology Ecology, Vol. 79, Issue 2 https://doi.org/10.1111/j.1574-6941.2011.01235.x	journal	November 2011
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
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
Genome sequence of the -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia Amadou, C.; Pascal, G.; Mangenot, S. Genome Research, Vol. 18, Issue 9 https://doi.org/10.1101/gr.076448.108	journal	July 2008
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
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
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
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
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
Novel strains of nodulating Burkholderia have a role in nitrogen fixation with papilionoid herbaceous legumes adapted to acid, infertile soils Garau, Giovanni; Yates, Ron J.; Deiana, Pietrino Soil Biology and Biochemistry, Vol. 41, Issue 1 https://doi.org/10.1016/j.soilbio.2008.10.011	journal	January 2009
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
Burkholderia and Cupriavidus spp. are the preferred symbionts of Mimosa spp. in Southern China Liu, XiaoYun; Wei, Shuang; Wang, Fang FEMS Microbiology Ecology, Vol. 80, Issue 2 https://doi.org/10.1111/j.1574-6941.2012.01310.x	journal	February 2012
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
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
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
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
Novel Burkholderia bacteria isolated from Lebeckia ambigua – A perennial suffrutescent legume of the fynbos Howieson, John G.; De Meyer, Sofie E.; Vivas-Marfisi, Anabel Soil Biology and Biochemistry, Vol. 60 https://doi.org/10.1016/j.soilbio.2013.01.009	journal	May 2013
South African Papilionoid Legumes Are Nodulated by Diverse Burkholderia with Unique Nodulation and Nitrogen-Fixation Loci Beukes, Chrizelle W.; Venter, Stephanus N.; Law, Ian J. PLoS ONE, Vol. 8, Issue 7 https://doi.org/10.1371/journal.pone.0068406	journal	July 2013
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil dos Reis Jr, Fábio Bueno; Simon, Marcelo F.; Gross, Eduardo New Phytologist, Vol. 186, Issue 4 https://doi.org/10.1111/j.1469-8137.2010.03267.x	journal	April 2010
Housing temperature influences exercise training adaptations in mice Raun, Steffen H.; Henriquez-Olguín, Carlos; Karavaeva, Iuliia Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15311-y	journal	March 2020
Validation of publication of new names and new combinations previously effectively published outside the IJSEM International Journal of Systematic and Evolutionary Microbiology, Vol. 50, Issue 4, p. 1415-1417 https://doi.org/10.1099/00207713-50-4-1415	journal	July 2000
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
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
Cupriavidus necator gen. nov., sp. nov.; a Nonobligate Bacterial Predator of Bacteria in Soil Makkar, N. S.; Casida, L. E. International Journal of Systematic Bacteriology, Vol. 37, Issue 4 https://doi.org/10.1099/00207713-37-4-323	journal	October 1987
Monophyly of nodA and nifH Genes across Texan and Costa Rican Populations of Cupriavidus Nodule Symbionts Andam, C. P.; Mondo, S. J.; Parker, M. A. Applied and Environmental Microbiology, Vol. 73, Issue 14 https://doi.org/10.1128/aem.00160-07	journal	May 2007
New Betaproteobacterial Rhizobium Strains Able To Efficiently Nodulate Parapiptadenia rigida (Benth.) Brenan Taulé, Cecilia; Zabaleta, María; Mareque, Cintia Applied and Environmental Microbiology, Vol. 78, Issue 6 https://doi.org/10.1128/aem.06215-11	journal	January 2012

Cited By (4)

Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Kaye BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6623-z	journal	March 2020
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Research Square [preprints] https://doi.org/10.21203/rs.2.15865/v4	posted_content	February 2020
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Kaye Research Square [preprints] https://doi.org/10.21203/rs.2.15865/v5	posted_content	March 2020
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Research Square [preprints] https://doi.org/10.21203/rs.2.15865/v3	posted_content	March 2020

Similar Records

Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil

Journal Article · Fri Mar 06 00:00:00 EST 2020 · BMC Genomics · OSTI ID:1256939

Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Kaye; +12 more

High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

Journal Article · Tue Jan 17 00:00:00 EST 2017 · Standards in Genomic Sciences · OSTI ID:1256939

Klonowska, Agnieszka; López-López, Aline; Moulin, Lionel; +15 more

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512

Journal Article · Sat Apr 11 00:00:00 EDT 2015 · Standards in Genomic Sciences · OSTI ID:1256939

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui; +10 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Root-nodule bacteria
Nitrogen fixation
Betaproteobacteria
Texas
Mimosa asperata
GEBA-RNB

Title: High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

Citation Formats

References (42)

Cited By (4)

Similar Records

Related Subjects