Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China
Abstract
Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125T was isolated from a hypersaline lake in China. The genome of strain YIM 91125T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.
- Authors:
-
- Chinese Academy of Sciences (CAS), Urumqi,(China). Xinjiang Institute of Ecology and Geography; Univ. of Chinese Academy of Sciences, Beijing (China)
- Yunnan Univ., Kunming (China)
- Yunnan Univ., Kunming (China); Qujing Affiliated Hospital of Kunming Medical University, Qujing (China)
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang (China)
- St. Petersburg State Univ., St. Petersburg (Russia). Theodosius Dobzhansky Center for Genome Bionformatics; St. Petersburg Academic Univ., St. Petersburg (Russia)
- DOE Joint Genome Institute, Walnut Creek, CA (United States)
- Leibniz Inst. DSMZ, Braunschweig (Germany)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Leibniz Inst. DSMZ, Braunschweig (Germany); Newcastle Univ. Newcastle upon Tyne (United Kingdom)
- DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
- Chinese Academy of Sciences (CAS), Urumqi,(China). Xinjiang Institute of Ecology and Geography; Yunnan Univ., Kunming (China)
- 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:
- 1256080
- 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; Halomonas lutea; Aerobic; Gram-negative; Chemoorganotrophic; Moderately halophilic; Lake Ebinur
Citation Formats
Gao, Xiao-Yang, Zhi, Xiao-Yang, Li, Hong-Wei, Zhou, Yu, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China. United States: N. p., 2015.
Web. doi:10.1186/1944-3277-10-1.
Gao, Xiao-Yang, Zhi, Xiao-Yang, Li, Hong-Wei, Zhou, Yu, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., & Li, Wen-Jun. Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China. United States. https://doi.org/10.1186/1944-3277-10-1
Gao, Xiao-Yang, Zhi, Xiao-Yang, Li, Hong-Wei, Zhou, Yu, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Mavromatis, Konstantinos, Tindall, Brian J., Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. Tue .
"Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China". United States. https://doi.org/10.1186/1944-3277-10-1. https://www.osti.gov/servlets/purl/1256080.
@article{osti_1256080,
title = {Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China},
author = {Gao, Xiao-Yang and Zhi, Xiao-Yang and Li, Hong-Wei and Zhou, Yu and Lapidus, Alla and Han, James and Haynes, Matthew and Lobos, Elizabeth and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia N. and Mavromatis, Konstantinos and Tindall, Brian J. and Markowitz, Victor and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C. and Li, Wen-Jun},
abstractNote = {Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125T was isolated from a hypersaline lake in China. The genome of strain YIM 91125T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.},
doi = {10.1186/1944-3277-10-1},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {Tue Jan 20 00:00:00 EST 2015},
month = {Tue Jan 20 00:00:00 EST 2015}
}
Web of Science
Works referenced in this record:
A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence
journal, November 2012
- Balasubramanian, Deepak; Schneper, Lisa; Kumari, Hansi
- Nucleic Acids Research, Vol. 41, Issue 1
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
Shifting the genomic gold standard for the prokaryotic species definition
journal, October 2009
- Richter, Michael; Rosselló-Móra, Ramon
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water
journal, April 2007
- Kim, K. K.; Jin, L.; Yang, H. C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 4
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
How Many Bootstrap Replicates Are Necessary?
journal, March 2010
- Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
- Journal of Computational Biology, Vol. 17, Issue 3
Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain
journal, February 2007
- Cabrera, A.; Aguilera, M.; Fuentes, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 2
Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium
journal, June 2007
- Wang, Y. -N.; Cai, H.; Chi, C. -Q.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 6
The DNA Bank Network: The Start from a German Initiative
journal, March 2011
- Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
- Biopreservation and Biobanking, Vol. 9, Issue 1
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
journal, November 2011
- Kim, O. -S.; Cho, Y. -J.; Lee, K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 3
Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence
journal, July 2000
- Anzai, Y.; Kim, H.; Park, J. Y.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 4
Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico
journal, May 2007
- Soto-Ramirez, N.; Sanchez-Porro, C.; Rosas, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 5
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010
- Gnerre, S.; MacCallum, I.; Przybylski, D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011
- Tamura, K.; Peterson, D.; Peterson, N.
- Molecular Biology and Evolution, Vol. 28, Issue 10
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
journal, January 2010
- Auch, Alexander F.; Klenk, Hans-Peter; Göker, Markus
- Standards in Genomic Sciences, Vol. 2, Issue 1
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea
journal, October 2007
- Jeon, C. O.; Lim, J. -M.; Lee, J. R.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 10
Gene Ontology: tool for the unification of biology
journal, May 2000
- Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
- Nature Genetics, Vol. 25, Issue 1
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011
- Pagani, I.; Liolios, K.; Jansson, J.
- Nucleic Acids Research, Vol. 40, Issue D1
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
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
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
journal, January 2010
- Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter
- Standards in Genomic Sciences, Vol. 2, Issue 1
Halomonas muralis sp. nov., isolated from microbial biofilms colonizing the walls and murals of the Saint-Catherine chapel (Castle Herberstein, Austria)
journal, November 2002
- Heyrman, J.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 6
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012
- Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S.
- PLoS ONE, Vol. 7, Issue 12
Halomonas lutea sp. nov., a moderately halophilic bacterium isolated from a salt lake
journal, September 2008
- Wang, Y.; Tang, S. -K.; Lou, K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 9
Multiple sequence alignment using partial order graphs
journal, March 2002
- Lee, C.; Grasso, C.; Sharlow, M. F.
- Bioinformatics, Vol. 18, Issue 3
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010
- Klenk, H. -P.; Göker, M.
- Systematic and Applied Microbiology, Vol. 33, Issue 4
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009
- Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
- Nature, Vol. 462, Issue 7276
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010
- Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
- Nature Methods, Vol. 7, Issue 6
Phylogeny of the family Halomonadaceae based on 23S and 165 rDNA sequence analyses.
journal, January 2002
- Arahal, David R.; Ludwig, Wolfgang; Schleifer, Karl H.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 1
Biology of Moderately Halophilic Aerobic Bacteria
journal, June 1998
- Ventosa, Antonio; Nieto, Joaquín J.; Oren, Aharon
- Microbiology and Molecular Biology Reviews, Vol. 62, Issue 2
Characterization of a Haloalkalophilic Strictly Aerobic Bacterium, Isolated from Pantelleria Island
journal, October 1996
- Romano, Ida; Nicolaus, Barbara; Lama, Licia
- Systematic and Applied Microbiology, Vol. 19, Issue 3
Validation of publication of new names and new combinations previously effectively published outside the IJSEM
journal, November 2005
- Euzeby, Jean
- International Journal of Systematic and Evolutionary Microbiology, Vol. 55, Issue 6, p. 2235-2238
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
journal, September 1996
- Strimmer, K.; von Haeseler, A.
- Molecular Biology and Evolution, Vol. 13, Issue 7
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.
- Standards in Genomic Sciences, Vol. 9, Issue 3
Genome Sequence of
Halomonas
sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments
journal, October 2013
- Koechler, Sandrine; Plewniak, Frédéric; Barbe, Valérie
- Genome Announcements, Vol. 1, Issue 5
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass
journal, February 2020
- Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai
- Molecular Biology Reports, Vol. 47, Issue 3
En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010
- Klenk, H. -P.; Göker, M.
- Systematic and Applied Microbiology, Vol. 33, Issue 4
Halomonadaceae fam. nov., a New Family of the Class Proteobacteria to Accommodate the Genera Halomonas and Deleya
journal, November 1988
- Franzmann, Peter D.; Wehmeyer, Uta; Stackebrandt, Erko
- Systematic and Applied Microbiology, Vol. 11, Issue 1
Halomonas desiderata sp. nov, a new alkaliphilic, halotolerant and denitrifying bacterium isolated from a municipal sewage works
journal, August 1996
- Berendes, F.; Gottschalk, G.; Heine-Dobbernack, E.
- Systematic and Applied Microbiology, Vol. 19, Issue 2
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009
- Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
- Nature, Vol. 462, Issue 7276
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010
- Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
- Nature Methods, Vol. 7, Issue 6
Dietary palmitic acid promotes a prometastatic memory via Schwann cells
journal, November 2021
- Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc
- Nature, Vol. 599, Issue 7885
Shifting the genomic gold standard for the prokaryotic species definition
journal, October 2009
- Richter, Michael; Rosselló-Móra, Ramon
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010
- Gnerre, S.; MacCallum, I.; Przybylski, D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
The DNA Bank Network: The Start from a German Initiative
journal, March 2011
- Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
- Biopreservation and Biobanking, Vol. 9, Issue 1
How Many Bootstrap Replicates Are Necessary?
journal, March 2010
- Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
- Journal of Computational Biology, Vol. 17, Issue 3
Multiple sequence alignment using partial order graphs
journal, March 2002
- Lee, C.; Grasso, C.; Sharlow, M. F.
- Bioinformatics, Vol. 18, Issue 3
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011
- Pagani, I.; Liolios, K.; Jansson, J.
- Nucleic Acids Research, Vol. 40, Issue D1
A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence
journal, November 2012
- Balasubramanian, Deepak; Schneper, Lisa; Kumari, Hansi
- Nucleic Acids Research, Vol. 41, Issue 1
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
journal, September 1996
- Strimmer, K.; von Haeseler, A.
- Molecular Biology and Evolution, Vol. 13, Issue 7
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
journal, July 1987
- Saitou, N.; Nei, M.
- Molecular Biology and Evolution, Vol. 4, Issue 4, p. 406-425
Halomonas elongata, a New Genus and Species of Extremely Salt-Tolerant Bacteria
journal, April 1980
- Vreeland, R. H.; Litchfield, C. D.; Martin, E. L.
- International Journal of Systematic Bacteriology, Vol. 30, Issue 2
Phylogenetic Inferences and Taxonomic Consequences of 16S Ribosomal DNA Sequence Comparison of Chromohalobacter marismortui, Volcaniella eurihalina, and Deleya salina and Reclassification of V. eurihalina as Halomonas eurihalina comb. nov.
journal, October 1995
- Mellado, E.; Moore, E. R. B.; Nieto, J. J.
- International Journal of Systematic Bacteriology, Vol. 45, Issue 4
Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence
journal, July 2000
- Anzai, Y.; Kim, H.; Park, J. Y.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 4
Phylogeny of the family Halomonadaceae based on 23S and 165 rDNA sequence analyses.
journal, January 2002
- Arahal, David R.; Ludwig, Wolfgang; Schleifer, Karl H.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 1
Halomonas muralis sp. nov., isolated from microbial biofilms colonizing the walls and murals of the Saint-Catherine chapel (Castle Herberstein, Austria)
journal, November 2002
- Heyrman, J.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 6
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
journal, November 2011
- Kim, O. -S.; Cho, Y. -J.; Lee, K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 3
Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain
journal, February 2007
- Cabrera, A.; Aguilera, M.; Fuentes, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 2
Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water
journal, April 2007
- Kim, K. K.; Jin, L.; Yang, H. C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 4
Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico
journal, May 2007
- Soto-Ramirez, N.; Sanchez-Porro, C.; Rosas, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 5
Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium
journal, June 2007
- Wang, Y. -N.; Cai, H.; Chi, C. -Q.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 6
Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea
journal, October 2007
- Jeon, C. O.; Lim, J. -M.; Lee, J. R.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 10
Halomonas lutea sp. nov., a moderately halophilic bacterium isolated from a salt lake
journal, September 2008
- Wang, Y.; Tang, S. -K.; Lou, K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 9
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
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
- Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S.
- PLoS ONE, Vol. 7, Issue 12
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
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
journal, January 2010
- Auch, Alexander F.; Klenk, Hans-Peter; Göker, Markus
- Standards in Genomic Sciences, Vol. 2, Issue 1
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
Works referencing / citing this record:
Complete genome sequence of the halophilic PHA-producing bacterium Halomonas sp. SF2003: insights into its biotechnological potential
journal, March 2019
- Thomas, Tatiana; Elain, Anne; Bazire, Alexis
- World Journal of Microbiology and Biotechnology, Vol. 35, Issue 3
Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants
journal, March 2018
- Montanari-Coelho, Katiúscia Kelli; Costa, Alessandra Tenório; Polonio, Julio Cesar
- World Journal of Microbiology and Biotechnology, Vol. 34, Issue 4
Enhanced long-term nitrogen removal by organotrophic anammox bacteria under different C/N ratio constraints: quantitative molecular mechanism and microbial community dynamics
journal, January 2016
- Shu, Duntao; He, Yanling; Yue, Hong
- RSC Advances, Vol. 6, Issue 90
Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution
journal, July 2018
- Boddicker, Andrew M.; Mosier, Annika C.
- The ISME Journal, Vol. 12, Issue 12
Exploring the unmapped DNA and RNA reads in a songbird genome
journal, January 2019
- Laine, Veronika N.; Gossmann, Toni I.; van Oers, Kees
- BMC Genomics, Vol. 20, Issue 1
The MG-RAST metagenomics database and portal in 2015
journal, December 2015
- Wilke, Andreas; Bischof, Jared; Gerlach, Wolfgang
- Nucleic Acids Research, Vol. 44, Issue D1
Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan
journal, July 2019
- Sakai, Hiroyuki D.; Kurosawa, Norio
- BMC Research Notes, Vol. 12, Issue 1
Characterization of rhizobia isolates obtained from nodules of wild genotypes of common bean
journal, January 2017
- Cardoso, Aline Assis; Andraus, Michel de Paula; Borba, Tereza Cristina de Oliveira
- Brazilian Journal of Microbiology, Vol. 48, Issue 1
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials
journal, June 2017
- Gómez-Garzón, Camilo; Hernández-Santana, Alejandra; Dussán, Jenny
- PLOS ONE, Vol. 12, Issue 6