High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

Laviad, Sivan; Lapidus, Alla; Han, James; Haynes, Matthew; Reddy, TBK; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia N.; Mavromatis, Konstantinos; Lang, Elke; Rohde, Manfred; Markowitz, Victor; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C.; Halpern, Malka

doi:10.1186/s40793-015-0010-4

Title: High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

Journal Article · Wed May 27 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0010-4· OSTI ID:1256917

Laviad, Sivan ^[1]; Lapidus, Alla ^[2]; Han, James ^[3]; Haynes, Matthew ^[3]; Reddy, TBK ^[3]; Huntemann, Marcel ^[3]; Pati, Amrita ^[3]; Ivanova, Natalia N. ^[3]; Mavromatis, Konstantinos ^[3]; Lang, Elke ^[4]; Rohde, Manfred ^[5]; Markowitz, Victor ^[6]; Woyke, Tanja ^[3]; Klenk, Hans-Peter ^[4]; Kyrpides, Nikos C. ^[7]; Halpern, Malka ^[1]

Univ. of Haifa (Israel)
St. Peterburg State Univ. (Russia); St. Petersburg Academic Univ. (Russia)
DOE Joint Genome Inst., Walnut Creek, CA (United States)
Leibniz-Inst. DSMZ, Braunschweig (Germany)
Helmholz Centre for Infection Research, Braunschweig (Germany)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
DOE Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

Brachymonas chironomi strain AIMA4T (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequences placed strain AIMA4T in the genus Brachymonas. Here we describe the features of this organism, together with the complete genome sequence and annotation. We find the DNA GC content is 63.5%. The chromosome length is 2,509,395 bp. It encodes 2,382 proteins and 68 RNA genes. Brachymonas chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

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

OSTI ID:: 1256917

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

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 1 work

Citation information provided by
Web of Science

References (43)

Brachymonas denitrificans gen. nov., sp. nov., an aerobic chemoorganotrophic bacterium which contains rhodoquinones, and evolutionary relationships of rhodoquinone producers to bacterial species with various quinone classes. Hiraishi, Akira; Sugiyama, Junta; Shin, Yong Kook The Journal of General and Applied Microbiology, Vol. 41, Issue 2 https://doi.org/10.2323/jgam.41.99	journal	January 1995
Brachymonas chironomi sp. nov., isolated from a chironomid egg mass, and emended description of the genus Brachymonas Halpern, M.; Shaked, T.; Schumann, P. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 12 https://doi.org/10.1099/ijs.0.007211-0	journal	July 2009
Culturable and VBNC Vibrio cholerae: Interactions with Chironomid Egg Masses and Their Bacterial Population Halpern, Malka; Landsberg, Ori; Raats, Dina Microbial Ecology, Vol. 53, Issue 2 https://doi.org/10.1007/s00248-006-9094-0	journal	December 2006
Chironomid egg masses and Vibrio cholerae Broza, Meir; Halpern, Malka Nature, Vol. 412, Issue 6842 https://doi.org/10.1038/35083691	journal	July 2001
Chironomid Egg Masses as a Natural Reservoir of Vibrio cholerae Non-O1 and Non-O139 in Freshwater Habitats Halpern, M.; Broza, Y. B.; Mittler, S. Microbial Ecology, Vol. 47, Issue 4 https://doi.org/10.1007/s00248-003-2007-6	journal	December 2003
Dependent population dynamics between chironomids (nonbiting midges) and Vibrio cholerae: Chironomids and Vibrio cholerae Halpern, Malka; Raats, Dina; Lavion, Revital FEMS Microbiology Ecology, Vol. 55, Issue 1 https://doi.org/10.1111/j.1574-6941.2005.00020.x	journal	January 2006
Vibrio cholerae and Aeromonas: do they share a mutual host? Senderovich, Yigal; Gershtein, Yana; Halewa, Etti The ISME Journal, Vol. 2, Issue 3 https://doi.org/10.1038/ismej.2007.114	journal	February 2008
Re-identification of Aeromonas isolates from chironomid egg masses as the potential pathogenic bacteria Aeromonas aquariorum: Aeromonas aquarirum in chironomid eggs Figueras, Maria José; Beaz-Hidalgo, Roxana; Senderovich, Yigal Environmental Microbiology Reports, Vol. 3, Issue 2 https://doi.org/10.1111/j.1758-2229.2010.00216.x	journal	October 2010
Chironomid egg masses harbour the clinical species Aeromonas taiwanensis and Aeromonas sanarellii Beaz-Hidalgo, Roxana; Shakèd, Tamar; Laviad, Sivan FEMS Microbiology Letters, Vol. 337, Issue 1 https://doi.org/10.1111/1574-6968.12003	journal	October 2012
Novel insights into Haemagglutinin Protease (HAP) gene regulation in Vibrio cholerae Halpern, Malka Molecular Ecology, Vol. 19, Issue 19 https://doi.org/10.1111/j.1365-294X.2010.04809.x	journal	September 2010
Oceanobacillus chironomi sp. nov., a halotolerant and facultatively alkaliphilic species isolated from a chironomid egg mass Raats, Dina; Halpern, Malka International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 2 https://doi.org/10.1099/ijs.0.64502-0	journal	February 2007
Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass Halpern, Malka; Senderovich, Yigal; Snir, Sagi International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 8 https://doi.org/10.1099/ijs.0.64927-0	journal	August 2007
Polyphasic Taxonomic Study of the Emended Genus Comamonas: Relationship to Aquaspirillum aquaticum, E. Falsen Group 10, and Other Clinical Isolates Willems, A.; Pot, B.; Falsen, E. International Journal of Systematic Bacteriology, Vol. 41, Issue 3 https://doi.org/10.1099/00207713-41-3-427	journal	July 1991
Permanent draft genome sequence of Comamonas testosteroni KF-1 Weiss, Michael; Kesberg, Anna I.; LaButti, Kurt M. Standards in Genomic Sciences, Vol. 8, Issue 2 https://doi.org/10.4056/sigs.3847890	journal	May 2013
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos Nature, Vol. 462, Issue 7276 https://doi.org/10.1038/nature08656	journal	December 2009
En route to a genome-based classification of Archaea and Bacteria? Klenk, H. -P.; Göker, M. Systematic and Applied Microbiology, Vol. 33, Issue 4 https://doi.org/10.1016/j.syapm.2010.03.003	journal	June 2010
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects Göker, Markus; Klenk, Hans-Peter Standards in Genomic Sciences, Vol. 8, Issue 2 https://doi.org/10.4056/sigs.3446951	journal	May 2013
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A. Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.5068949	journal	December 2013
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A. PLoS Biology, Vol. 12, Issue 8 https://doi.org/10.1371/journal.pbio.1001920	journal	August 2014
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 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
The DNA Bank Network: The Start from a German Initiative Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger Biopreservation and Biobanking, Vol. 9, Issue 1 https://doi.org/10.1089/bio.2010.0029	journal	March 2011
Solexa Ltd Bennett, Simon Pharmacogenomics, Vol. 5, Issue 4 https://doi.org/10.1517/14622416.5.4.433	journal	June 2004
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
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
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 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
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
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
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
The protective role of endogenous bacterial communities in chironomid egg masses and larvae Senderovich, Yigal; Halpern, Malka The ISME Journal, Vol. 7, Issue 11 https://doi.org/10.1038/ismej.2013.100	journal	June 2013
The Chironomidae Armitage, Patrick D.; Cranston, Peter S.; Pinder, L. C. V. Springer Dordrecht https://doi.org/10.1007/978-94-011-0715-0	book	January 1995
Bacterial Community Composition Associated with Chironomid Egg Masses Senderovich, Yigal; Halpern, Malka Journal of Insect Science, Vol. 12, Issue 149 https://doi.org/10.1673/031.012.14901	journal	December 2012
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
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
Class I. Alphaproteobacteria class. nov. Garrity, George M.; Bell, Julia A.; Lilburn, Timothy Bergey’s Manual® of Systematic Bacteriology https://doi.org/10.1007/0-387-29298-5_1	book	January 2005
Class II. Betaproteobacteria class. nov. Garrity, George M.; Bell, Julia A.; Lilburn, Timothy Bergey’s Manual® of Systematic Bacteriology https://doi.org/10.1007/0-387-29298-5_2	book	January 2005
NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969) Willems, A.; De Ley, J.; Gillis, M. International Journal of Systematic Bacteriology, Vol. 41, Issue 3 https://doi.org/10.1099/00207713-41-3-445	journal	July 1991
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
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
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
Vibrio cholerae Hemagglutinin/Protease Degrades Chironomid Egg Masses Halpern, Malka; Gancz, Hanan; Broza, Meir Applied and Environmental Microbiology, Vol. 69, Issue 7 https://doi.org/10.1128/aem.69.7.4200-4204.2003	journal	July 2003

Cited By (1)

Exemplar Abstract for Brachymonas chironomi Halpern et al. 2009. Parker, Charles Thomas; Taylor, Dorothea; Garrity, George M. NamesforLife https://doi.org/10.1601/ex.14920	dataset	January 2013

Figures / Tables (5)

Similar Records

High quality draft genome sequence of Leucobacter chironomi strain MM2LBT (DSM 19883T) isolated from a Chironomus sp. egg mass

Journal Article · Fri May 08 00:00:00 EDT 2015 · Standards in Genomic Sciences · OSTI ID:1256917

Laviad, Sivan; Lapidus, Alla; Copeland, Alex; +10 more

Effects of sediment bioturbation by Chironomus tentans on toxicity of heavy metals to Ceriodaphnia dubia

Conference · Sat Dec 31 00:00:00 EST 1994 · OSTI ID:1256917

Pearson, M S; Clements, W H

High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775^T, a plant pathogen of French bean pods

Journal Article · Wed Jan 13 00:00:00 EST 2016 · Standards in Genomic Sciences · OSTI ID:1256917

Aizenberg-Gershtein, Yana; Izhaki, Ido; Lapidus, Alla; +10 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Brachymonas chironomi
Comamonadaceae
Chironomid
Chironomus
Egg mass
Toxicant