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

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

doi:10.1186/s40793-015-0010-4

High quality draft genome sequence of brachymonas chironomi AIMA4^T (DSM 19884^T) isolated from a chironomus sp. egg mass

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

Research output: Contribution to journal › Article › peer-review

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. 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.

Original language	English
Journal	Standards in Genomic Sciences
Volume	10
Issue number	MAY2015
DOIs	https://doi.org/10.1186/s40793-015-0010-4
State	Published - 1 May 2015

Bibliographical note

Funding Information:
We would like to gratefully acknowledge the help of Nicole Reimann for growing B. chironomi cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 Genome analysis was supported by the National Basic Research Program of China (No. 2010CB833801). A.L. was supported in part by Russian Ministry of Science Mega-grant no.11.G34.31.0068 (PI Dr Stephen J O’Brien). M. H. was supported in part by a grant from the US Civilian Research and Development Foundation (CRDF grant no. ILB1-7045-HA).

Publisher Copyright:
© 2015 Laviad et al.

Keywords

Brachymonas chironomi
Chironomid
Chironomus
Comamonadaceae
Egg mass
Toxicant

ASJC Scopus subject areas

Genetics

Access to Document

10.1186/s40793-015-0010-4

Cite this

Laviad, S., Lapidus, A., Han, J., Haynes, M., Reddy, T. B. K., Huntemann, M., Pati, A., Ivanova, N. N., Mavromatis, K., Lang, E., Rohde, M., Markowitz, V., Woyke, T., Klenk, H. P., Kyrpides, N. C., & Halpern, M. (2015). High quality draft genome sequence of brachymonas chironomi AIMA4^T (DSM 19884^T) isolated from a chironomus sp. egg mass. Standards in Genomic Sciences, 10(MAY2015). https://doi.org/10.1186/s40793-015-0010-4

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title = "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. 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.",

keywords = "Brachymonas chironomi, Chironomid, Chironomus, Comamonadaceae, Egg mass, Toxicant",

author = "Sivan Laviad and Alla Lapidus and James Han and Matthew Haynes and Reddy, {T. B.K.} and Marcel Huntemann and Amrita Pati and Ivanova, {Natalia N.} and Konstantinos Mavromatis and Elke Lang and Manfred Rohde and Victor Markowitz and Tanja Woyke and Klenk, {Hans Peter} and Kyrpides, {Nikos C.} and Malka Halpern",

note = "Funding Information: We would like to gratefully acknowledge the help of Nicole Reimann for growing B. chironomi cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 Genome analysis was supported by the National Basic Research Program of China (No. 2010CB833801). A.L. was supported in part by Russian Ministry of Science Mega-grant no.11.G34.31.0068 (PI Dr Stephen J O{\textquoteright}Brien). M. H. was supported in part by a grant from the US Civilian Research and Development Foundation (CRDF grant no. ILB1-7045-HA). Publisher Copyright: {\textcopyright} 2015 Laviad et al.",

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Laviad, S, Lapidus, A, Han, J, Haynes, M, Reddy, TBK, Huntemann, M, Pati, A, Ivanova, NN, Mavromatis, K, Lang, E, Rohde, M, Markowitz, V, Woyke, T, Klenk, HP, Kyrpides, NC & Halpern, M 2015, 'High quality draft genome sequence of brachymonas chironomi AIMA4^T (DSM 19884^T) isolated from a chironomus sp. egg mass', Standards in Genomic Sciences, vol. 10, no. MAY2015. https://doi.org/10.1186/s40793-015-0010-4

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T1 - High quality draft genome sequence of brachymonas chironomi AIMA4T (DSM 19884T) isolated from a chironomus sp. egg mass

AU - Laviad, Sivan

AU - Lapidus, Alla

AU - Han, James

AU - Haynes, Matthew

AU - Reddy, T. B.K.

AU - Huntemann, Marcel

AU - Pati, Amrita

AU - Ivanova, Natalia N.

AU - Mavromatis, Konstantinos

AU - Lang, Elke

AU - Rohde, Manfred

AU - Markowitz, Victor

AU - Woyke, Tanja

AU - Klenk, Hans Peter

AU - Kyrpides, Nikos C.

AU - Halpern, Malka

N1 - Funding Information: We would like to gratefully acknowledge the help of Nicole Reimann for growing B. chironomi cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 Genome analysis was supported by the National Basic Research Program of China (No. 2010CB833801). A.L. was supported in part by Russian Ministry of Science Mega-grant no.11.G34.31.0068 (PI Dr Stephen J O’Brien). M. H. was supported in part by a grant from the US Civilian Research and Development Foundation (CRDF grant no. ILB1-7045-HA). Publisher Copyright: © 2015 Laviad et al.

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N2 - 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. 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.

AB - 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. 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.

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