High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea
Abstract
Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the degradation of industrial effluents. Here, the characteristics and the permanent-draft genome sequence and annotation of Halotalea alkalilenta AW-7T are described. The microorganism was sequenced as a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome Institute, and it is the only strain within the genus Halotalea having its genome sequenced. The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC content. A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes. Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea alkalilenta AW-7T encodes the catechol and protocatechuate degradation to β-ketoadipate via the β-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. Lastly, an emended description of the genus Halotalea Ntougias et al. 2007 is also provided in order to describe the delayed fermentation ability of the type strain.
- Authors:
-
- Democritus Univ. of Thrace, Xanthi (Greece)
- St. Petersburg State Univ. (Russia)
- Dept. of Energy Joint Genome Inst., Walnut Creek, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Leibniz Inst. DSMZ, Braunschweig (Germany)
- Agricultural Univ., Athens (Greece)
- Dept. of Energy 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:
- 1256934
- Grant/Contract Number:
- AC02-05CH11231
- 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
Citation Formats
Ntougias, Spyridon, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Pati, Amrita, Ivanova, Natalia N., Markowitz, Victor M., Klenk, Hans-Peter, Woyke, Tanja, Fasseas, Constantinos, Kyrpides, Nikos C., and Zervakis, Georgios I. High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea. United States: N. p., 2015.
Web. doi:10.1186/s40793-015-0052-7.
Ntougias, Spyridon, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Pati, Amrita, Ivanova, Natalia N., Markowitz, Victor M., Klenk, Hans-Peter, Woyke, Tanja, Fasseas, Constantinos, Kyrpides, Nikos C., & Zervakis, Georgios I. High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea. United States. https://doi.org/10.1186/s40793-015-0052-7
Ntougias, Spyridon, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Pati, Amrita, Ivanova, Natalia N., Markowitz, Victor M., Klenk, Hans-Peter, Woyke, Tanja, Fasseas, Constantinos, Kyrpides, Nikos C., and Zervakis, Georgios I. Thu .
"High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea". United States. https://doi.org/10.1186/s40793-015-0052-7. https://www.osti.gov/servlets/purl/1256934.
@article{osti_1256934,
title = {High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea},
author = {Ntougias, Spyridon and Lapidus, Alla and Copeland, Alex and Reddy, T. B. K. and Pati, Amrita and Ivanova, Natalia N. and Markowitz, Victor M. and Klenk, Hans-Peter and Woyke, Tanja and Fasseas, Constantinos and Kyrpides, Nikos C. and Zervakis, Georgios I.},
abstractNote = {Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the degradation of industrial effluents. Here, the characteristics and the permanent-draft genome sequence and annotation of Halotalea alkalilenta AW-7T are described. The microorganism was sequenced as a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome Institute, and it is the only strain within the genus Halotalea having its genome sequenced. The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC content. A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes. Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea alkalilenta AW-7T encodes the catechol and protocatechuate degradation to β-ketoadipate via the β-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. Lastly, an emended description of the genus Halotalea Ntougias et al. 2007 is also provided in order to describe the delayed fermentation ability of the type strain.},
doi = {10.1186/s40793-015-0052-7},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {Thu Aug 13 00:00:00 EDT 2015},
month = {Thu Aug 13 00:00:00 EDT 2015}
}
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Figures / Tables:
Fig. 1: Phylogenetic tree displaying the position of H. alkalilenta AW-7T among the type strains of other species within the Halomonadaceae. The tree was inferred from 1152 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion. Tree branches are constructed on the basis of themore »
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The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012
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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
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013
- Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.
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The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
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- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
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Works referencing / citing this record:
Nomenclature Abstract for Halotalea Ntougias et al. 2007 emend. Ntougias et al. 2015.
dataset, January 2013
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- NamesforLife
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