High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway
Abstract
© 2016 Zhou et al. Thermus amyloliquefaciens type strain YIM 77409 T is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409 T together with its genome sequence and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with 67.4 % average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymes for heterotrophy highlight the broad heterotrophic lifestyle of this organism. A denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain.
- Authors:
- more »
- Publication Date:
- Research Org.:
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618965
- Alternate Identifier(s):
- OSTI ID: 1287554; OSTI ID: 1379110
- Grant/Contract Number:
- AC02-05CH11231; 2013DFA31980
- Resource Type:
- Published Article
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Thermus; Thermus amyloliquefaciens; Thermophiles; hot springs; denitrification; nitrate respiration; extreme thermophile; sp nov.; anaerobic growth; scotoductus; identification; bacterium; oshimai; springs; biology
Citation Formats
Zhou, En-Min, Murugapiran, Senthil K., Mefferd, Chrisabelle C., Liu, Lan, Xian, Wen-Dong, Yin, Yi-Rui, Ming, Hong, Yu, Tian-Tian, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Spunde, Alexander, Kyrpides, Nikos, Woyke, Tanja, Li, Wen-Jun, and Hedlund, Brian P. High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway. United Kingdom: N. p., 2016.
Web. doi:10.1186/s40793-016-0140-3.
Zhou, En-Min, Murugapiran, Senthil K., Mefferd, Chrisabelle C., Liu, Lan, Xian, Wen-Dong, Yin, Yi-Rui, Ming, Hong, Yu, Tian-Tian, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Spunde, Alexander, Kyrpides, Nikos, Woyke, Tanja, Li, Wen-Jun, & Hedlund, Brian P. High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway. United Kingdom. https://doi.org/10.1186/s40793-016-0140-3
Zhou, En-Min, Murugapiran, Senthil K., Mefferd, Chrisabelle C., Liu, Lan, Xian, Wen-Dong, Yin, Yi-Rui, Ming, Hong, Yu, Tian-Tian, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Spunde, Alexander, Kyrpides, Nikos, Woyke, Tanja, Li, Wen-Jun, and Hedlund, Brian P. Sat .
"High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway". United Kingdom. https://doi.org/10.1186/s40793-016-0140-3.
@article{osti_1618965,
title = {High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway},
author = {Zhou, En-Min and Murugapiran, Senthil K. and Mefferd, Chrisabelle C. and Liu, Lan and Xian, Wen-Dong and Yin, Yi-Rui and Ming, Hong and Yu, Tian-Tian and Huntemann, Marcel and Clum, Alicia and Pillay, Manoj and Palaniappan, Krishnaveni and Varghese, Neha and Mikhailova, Natalia and Stamatis, Dimitrios and Reddy, T. B. K. and Ngan, Chew Yee and Daum, Chris and Shapiro, Nicole and Markowitz, Victor and Ivanova, Natalia and Spunde, Alexander and Kyrpides, Nikos and Woyke, Tanja and Li, Wen-Jun and Hedlund, Brian P.},
abstractNote = {© 2016 Zhou et al. Thermus amyloliquefaciens type strain YIM 77409 T is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409 T together with its genome sequence and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with 67.4 % average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymes for heterotrophy highlight the broad heterotrophic lifestyle of this organism. A denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain.},
doi = {10.1186/s40793-016-0140-3},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United Kingdom},
year = {Sat Feb 27 00:00:00 EST 2016},
month = {Sat Feb 27 00:00:00 EST 2016}
}
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https://doi.org/10.1186/s40793-016-0140-3
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Works referenced in this record:
Dissimilatory Reduction of Fe(III) and Other Electron Acceptors by a Thermus Isolate
journal, March 1999
- Kieft, T. L.; Fredrickson, J. K.; Onstott, T. C.
- Applied and Environmental Microbiology, Vol. 65, Issue 3
Thermus tengchongensis sp. nov., isolated from a geothermally heated soil sample in Tengchong, Yunnan, south-west China
journal, October 2012
- Yu, Tian-Tian; Yao, Ji-Cheng; Ming, Hong
- Antonie van Leeuwenhoek, Vol. 103, Issue 3
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
Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01
journal, November 2011
- Gounder, Kamini; Brzuszkiewicz, Elzbieta; Liesegang, Heiko
- BMC Genomics, Vol. 12, Issue 1
Electron transfer kinetics of soluble fragments indicate a direct interaction between complex III and the caa3 oxidase in Thermus thermophilus
journal, January 2007
- Janzon, Julia; Ludwig, Bernd; Malatesta, Francesco
- IUBMB Life, Vol. 59, Issue 8
Measuring Nitrification, Denitrification, and Related Biomarkers in Terrestrial Geothermal Ecosystems
book, January 2011
- Dodsworth, Jeremy A.; Hungate, Bruce; de la Torre, José R.
- Research on Nitrification and Related Processes, Part A
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, February 2014
- Kim, M.; Oh, H. -S.; Park, S. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009
- Eid, John; Fehr, Adrian; Gray, Jeremy
- Science, Vol. 323, Issue 5910, p. 133-138
Thermozymes and Their Applications: A Review of Recent Literature and Patents
journal, January 2001
- Bruins, Marieke E.; Janssen, Anja E. M.; Boom, Remko M.
- Applied Biochemistry and Biotechnology, Vol. 90, Issue 2
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
Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE
journal, May 2007
- Cava, Felipe; Laptenko, Oleg; Borukhov, Sergei
- Molecular Microbiology, Vol. 64, Issue 3
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
journal, May 2013
- Chin, Chen-Shan; Alexander, David H.; Marks, Patrick
- Nature Methods, Vol. 10, Issue 6
Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile
journal, January 1969
- Brock, Thomas D.; Freeze, Hudson
- Journal of Bacteriology, Vol. 98, Issue 1
Identification of iron-reducing Thermus strains as Thermus scotoductus
journal, February 2004
- Balkwill, D. L.; Kieft, T. L.; Tsukuda, T.
- Extremophiles, Vol. 8, Issue 1
Approved Lists of Bacterial Names
journal, January 1980
- Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1
Anaerobic Growth, a Property Horizontally Transferred by an Hfr-Like Mechanism among Extreme Thermophiles
journal, June 1998
- Ramírez-Arcos, Sandra; Fernández-Herrero, Luis A.; Marín, Irma
- Journal of Bacteriology, Vol. 180, Issue 12
Microbial nitrate respiration – Genes, enzymes and environmental distribution
journal, August 2011
- Kraft, Beate; Strous, Marc; Tegetmeyer, Halina E.
- Journal of Biotechnology, Vol. 155, Issue 1
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
Isolation and characterization of a mixotrophic sulfur-oxidizing Thermus scotoductus
journal, February 2001
- Skirnisdottir, Sigurlaug; Hreggvidsson, Gudmundur O.; Holst, Olle
- Extremophiles, Vol. 5, Issue 1
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
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea: N-cycling in Great Basin hot springs
journal, June 2011
- Dodsworth, Jeremy A.; Hungate, Bruce A.; Hedlund, Brian P.
- Environmental Microbiology, Vol. 13, Issue 8
Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ∼80 °C hot springs in the US Great Basin: N2O production by Thermus thermophilus and T. oshimai
journal, September 2011
- Hedlund, B. P.; Mcdonald, A. I.; Lam, J.
- Geobiology, Vol. 9, Issue 6
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
Thermaerobacter composti sp. nov., a novel extremely thermophilic bacterium isolated from compost
journal, January 2009
- Yabe, Shuhei; Kato, Atsushi; Hazaka, Masaru
- The Journal of General and Applied Microbiology, Vol. 55, Issue 5
A New Type of NADH Dehydrogenase Specific for Nitrate Respiration in the Extreme Thermophile Thermus thermophilus
journal, July 2004
- Cava, Felipe; Zafra, Olga; Magalon, Axel
- Journal of Biological Chemistry, Vol. 279, Issue 44
Biochemical and regulatory properties of a respiratory island encoded by a conjugative plasmid in the extreme thermophile Thermus thermophilus
journal, January 2006
- Cava, F.; Berenguer, J.
- Biochemical Society Transactions, Vol. 34, Issue 1
Cultivation and characterization of thermophilic Nitrospira species from geothermal springs in the US Great Basin, China, and Armenia
journal, April 2013
- Edwards, Tara A.; Calica, Nicole A.; Huang, Dolores A.
- FEMS Microbiology Ecology, Vol. 85, Issue 2
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics
journal, October 1987
- Moore, W. E. C.; Stackebrandt, E.; Kandler, O.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 37, Issue 4
Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling
journal, February 2013
- Murugapiran, Senthil K.; Huntemann, Marcel; Wei, Chia-Lin
- Standards in Genomic Sciences, Vol. 7, Issue 3
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
journal, October 2014
- Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
- Nucleic Acids Research, Vol. 43, Issue D1
Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs
journal, November 2013
- Hamilton, Trinity L.; Koonce, Evangeline; Howells, Alta
- Applied and Environmental Microbiology, Vol. 80, Issue 2
Accelerated Profile HMM Searches
journal, October 2011
- Eddy, Sean R.
- PLoS Computational Biology, Vol. 7, Issue 10
Life in extreme environments
journal, February 2001
- Rothschild, Lynn J.; Mancinelli, Rocco L.
- Nature, Vol. 409, Issue 6823
A four-subunit cytochrome bc1 complex complements the respiratory chain of Thermus thermophilus
journal, June 2005
- Mooser, Daniela; Maneg, Oliver; Corvey, Carsten
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1708, Issue 2
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
The role of the nitrate respiration element of Thermus thermophilus in the control and activity of the denitrification apparatus
journal, February 2008
- Cava, Felipe; Zafra, Olga; da Costa, Milton S.
- Environmental Microbiology, Vol. 10, Issue 2
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
Arsenite oxidation and arsenate respiration by a new Thermus isolate
journal, November 2001
- Gihring, Thomas M.; Banfield, Jillian F.
- FEMS Microbiology Letters, Vol. 204, Issue 2
A thermophilic nitrate reductase is responsible for the strain specific anaerobic growth of Thermus thermophilus HB8
journal, March 1998
- Ramı́rez-Arcos, Sandra; Fernández-Herrero, Luis Angel; Berenguer, José
- Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, Vol. 1396, Issue 2
Thermus amyloliquefaciens sp. nov., isolated from a hot spring sediment sample
journal, August 2015
- Park, Dong-Jin; Hozzein, Wael N.; Kim, Chang-Jin
- International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 8
Transfer of Thermus ruber (Loginova et al. 1984), Thermus silvanus (Tenreiro et al. 1995), and Thermus chliarophilus (Tenreiro et al. 1995) to Meiothermus gen. nov. as Meiothermus ruber comb, nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus
journal, October 1999
- Nobre, M. Fernanda; Trüper, Hans G.; da Costa, Milton S.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 49, Issue 4
Infernal 1.0: inference of RNA alignments
journal, March 2009
- Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R.
- Bioinformatics, Vol. 25, Issue 10
Thermus scotoductus, sp. nov., a Pigment-Producing Thermophilic Bacterium from Hot Tap Water in Iceland and Including Thermus sp. X-1
journal, March 1994
- Kristjánsson, Jakob K.; Hjörleifsdóttir, Sigrídur; Marteinsson, Viggó Th.
- Systematic and Applied Microbiology, Vol. 17, Issue 1
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
journal, January 2007
- Klappenbach, Joel A.; Goris, Johan; Vandamme, Peter
- International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 1
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
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
The Deinococcus-Thermus Phylum and the Effect of rRNA Composition on Phylogenetic Tree Construction
journal, March 1989
- Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.
- Systematic and Applied Microbiology, Vol. 11, Issue 2