High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass
Abstract
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.
- Authors:
-
- 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)
- 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:
- 1256917
- Grant/Contract Number:
- AC02-05CH11231; AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Brachymonas chironomi; Comamonadaceae; Chironomid; Chironomus; Egg mass; Toxicant
Citation Formats
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., and Halpern, Malka. High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass. United States: N. p., 2015.
Web. doi:10.1186/s40793-015-0010-4.
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. High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass. United States. https://doi.org/10.1186/s40793-015-0010-4
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., and Halpern, Malka. Wed .
"High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass". United States. https://doi.org/10.1186/s40793-015-0010-4. https://www.osti.gov/servlets/purl/1256917.
@article{osti_1256917,
title = {High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass},
author = {Laviad, Sivan and Lapidus, Alla and Han, James and Haynes, Matthew and Reddy, TBK and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia N. and Mavromatis, Konstantinos and Lang, Elke and Rohde, Manfred and Markowitz, Victor and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C. and Halpern, Malka},
abstractNote = {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.},
doi = {10.1186/s40793-015-0010-4},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {Wed May 27 00:00:00 EDT 2015},
month = {Wed May 27 00:00:00 EDT 2015}
}
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Figures / Tables:
Figure 1 : Phylogenetic tree highlighting the position of Brachymonas chironomi relative to the type strains of the other species within the family Comamonadaceae. The sequence alignments were performed by using the CLUSTAL W program and the tree was generated using the maximum likelihood method in MEGA 5 software. Bootstrapmore »
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Vibrio cholerae and Aeromonas: do they share a mutual host?
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NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969)
journal, July 1991
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Brachymonas chironomi sp. nov., isolated from a chironomid egg mass, and emended description of the genus Brachymonas
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Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass
journal, August 2007
- Halpern, Malka; Senderovich, Yigal; Snir, Sagi
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Chironomid egg masses harbour the clinical species Aeromonas taiwanensis and Aeromonas sanarellii
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- Beaz-Hidalgo, Roxana; Shakèd, Tamar; Laviad, Sivan
- FEMS Microbiology Letters, Vol. 337, Issue 1
Re-identification of Aeromonas isolates from chironomid egg masses as the potential pathogenic bacteria Aeromonas aquariorum: Aeromonas aquarirum in chironomid eggs
journal, October 2010
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Vibrio cholerae
Hemagglutinin/Protease Degrades Chironomid Egg Masses
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Prodigal: prokaryotic gene recognition and translation initiation site identification
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Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
journal, August 2014
- Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.
- PLoS Biology, Vol. 12, Issue 8
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012
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- PLoS ONE, Vol. 7, Issue 12
Bacterial Community Composition Associated with Chironomid Egg Masses
journal, December 2012
- Senderovich, Yigal; Halpern, Malka
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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.
journal, January 1995
- Hiraishi, Akira; Sugiyama, Junta; Shin, Yong Kook
- The Journal of General and Applied Microbiology, Vol. 41, Issue 2
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
journal, May 2013
- Göker, Markus; Klenk, Hans-Peter
- Standards in Genomic Sciences, Vol. 8, Issue 2
Works referencing / citing this record:
Exemplar Abstract for Brachymonas chironomi Halpern et al. 2009.
dataset, January 2013
- Parker, Charles Thomas; Taylor, Dorothea; Garrity, George M.
- NamesforLife
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.