High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea

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.

doi:10.1186/s40793-015-0052-7

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

Journal Article · Thu Aug 13 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0052-7· OSTI ID:1256934

Ntougias, Spyridon ^[1]; Lapidus, Alla ^[2]; Copeland, Alex ^[3]; Reddy, T. B. K. ^[3]; Pati, Amrita ^[3]; Ivanova, Natalia N. ^[3]; Markowitz, Victor M. ^[4]; Klenk, Hans-Peter ^[5]; Woyke, Tanja ^[3]; Fasseas, Constantinos ^[6]; Kyrpides, Nikos C. ^[7]; Zervakis, Georgios I. ^[6]

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)

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.

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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

OSTI ID:: 1256934

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

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 1 work

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References (48)

Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996 Ntougias, Spyridon; Zervakis, Georgios I.; Fasseas, Constantinos International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 9 https://doi.org/10.1099/ijs.0.65078-0	journal	September 2007
Unification of the Genera Deleya (Baumann et al. 1983), Halomonas (Vreeland et al. 1980), and Halovibrio (Fendrich 1988) and the Species Paracoccus halodenitrificans (Robinson and Gibbons 1952) into a Single Genus, Halomonas, and Placement of the Genus Zymobacter in the Family Halomonadaceae Dobson, S. J.; Franzmann, P. D. International Journal of Systematic Bacteriology, Vol. 46, Issue 2 https://doi.org/10.1099/00207713-46-2-550	journal	April 1996
Modicisalibacter tunisiensis gen. nov., sp. nov., an aerobic, moderately halophilic bacterium isolated from an oilfield-water injection sample, and emended description of the family Halomonadaceae Franzmann et al. 1989 emend Dobson and Franzmann 1996 emend. Ntougias et al. 2007 Ben Ali Gam, Zouhaier; Abdelkafi, Slim; Casalot, Laurence International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 10 https://doi.org/10.1099/ijs.0.65088-0	journal	October 2007
Halomonas elongata, a New Genus and Species of Extremely Salt-Tolerant Bacteria Vreeland, R. H.; Litchfield, C. D.; Martin, E. L. International Journal of Systematic Bacteriology, Vol. 30, Issue 2 https://doi.org/10.1099/00207713-30-2-485	journal	April 1980
Classification of "Chromobacterium marismortui" in a New Genus, Chromohalobacter gen. nov., as Chromohalobacter marismortui comb. nov., nom. rev. Ventosa, A.; Gutierrez, M. C.; Garcia, M. T. International Journal of Systematic Bacteriology, Vol. 39, Issue 4 https://doi.org/10.1099/00207713-39-4-382	journal	October 1989
Carnimonas nigrificans gen. nov., sp. nov., a bacterial causative agent for black spot formation on cured meat products Garriga, M.; Ehrmann, M. A.; Arnau, J. International Journal of Systematic Bacteriology, Vol. 48, Issue 3 https://doi.org/10.1099/00207713-48-3-677	journal	July 1998
Proposal of Cobetia marina gen. nov., comb. nov., within the Family Halomonadaceae, to Include the Species Halomonas marina Arahal, David R.; Castillo, Ana M.; Ludwig, Wolfgang Systematic and Applied Microbiology, Vol. 25, Issue 2 https://doi.org/10.1078/0723-2020-00113	journal	January 2002
Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. Sanchez-Porro, C.; de la Haba, R. R.; Soto-Ramirez, N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 2 https://doi.org/10.1099/ijs.0.001461-0	journal	February 2009
Aidingimonas halophila gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt lake Wang, Y.; Tang, S. -K.; Lou, K. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 12 https://doi.org/10.1099/ijs.0.010264-0	journal	July 2009
Larsenia salina gen. nov., sp. nov., a new member of the family Halomonadaceae based on multilocus sequence analysis León, María José; Sánchez-Porro, Cristina; de la Haba, Rafael R. Systematic and Applied Microbiology, Vol. 37, Issue 7 https://doi.org/10.1016/j.syapm.2014.07.006	journal	October 2014
Corrigendum to “Larsenia salina gen. nov., sp. nov., a new member of the family Halomonadaceae based on multilocus sequence analysis” [Syst. Appl. Microbiol. 37 (October (7)) (2014) 480–487] León, María José; Sánchez-Porro, Cristina; de la Haba, Rafael R. Systematic and Applied Microbiology, Vol. 38, Issue 1 https://doi.org/10.1016/j.syapm.2014.11.001	journal	February 2015
List of new names and new combinations previously effectively, but not validly, published Oren, Aharon; Garrity, George M. International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_4 https://doi.org/10.1099/ijs.0.000178	journal	April 2015
Multilocus sequence analysis of the family Halomonadaceae de la Haba, Rafael R.; Márquez, M. Carmen; Papke, R. Thane International Journal of Systematic and Evolutionary Microbiology, Vol. 62, Issue Pt_3 https://doi.org/10.1099/ijs.0.032938-0	journal	March 2012
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB DeSantis, T. Z.; Hugenholtz, P.; Larsen, N. Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072 https://doi.org/10.1128/AEM.03006-05	journal	July 2006
An algorithm for suffix stripping Porter, M. F. Program, Vol. 14, Issue 3 https://doi.org/10.1108/eb046814	journal	March 1980
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
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
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
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku950	journal	October 2014
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
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
IMG: the integrated microbial genomes database and comparative analysis system Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1044	journal	December 2011
Multiple sequence alignment using partial order graphs Lee, C.; Grasso, C.; Sharlow, M. F. Bioinformatics, Vol. 18, Issue 3 https://doi.org/10.1093/bioinformatics/18.3.452	journal	March 2002
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
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
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
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
Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria Williams, K. P.; Kelly, D. P. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 8 https://doi.org/10.1099/ijs.0.049270-0	journal	January 2013
Oceanospirillales ord. nov. Garrity, George M.; Bell, Julia A.; Lilburn, Timothy Bergey’s Manual® of Systematic Bacteriology https://doi.org/10.1007/0-387-28022-7_8	book	January 2005
NOTES: Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 29 International Journal of Systematic Bacteriology, Vol. 39, Issue 2, p. 205-206 https://doi.org/10.1099/00207713-39-2-205	journal	April 1989
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
Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap Okamoto, Tomoyuki; Taguchi, Hiroshi; Nakamura, Katsumi Archives of Microbiology, Vol. 160, Issue 5 https://doi.org/10.1007/bf00252218	journal	November 1993
Halomonadaceae fam. nov., a New Family of the Class Proteobacteria to Accommodate the Genera Halomonas and Deleya Franzmann, Peter D.; Wehmeyer, Uta; Stackebrandt, Erko Systematic and Applied Microbiology, Vol. 11, Issue 1 https://doi.org/10.1016/s0723-2020(88)80043-2	journal	November 1988
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
List of new names and new combinations previously effectively, but not validly, published Oren, Aharon; Garrity, George M. International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 3 https://doi.org/10.1099/ijsem.0.002570	journal	March 2018
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

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Nomenclature Abstract for Halotalea Ntougias et al. 2007 emend. Ntougias et al. 2015. NamesforLife https://doi.org/10.1601/nm.11348	dataset	January 2013