Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism
© The Author(s). 2017
Received: 24 November 2016
Accepted: 23 December 2016
Published: 3 February 2017
Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures. Here we analyze the first whole genome sequence of T. brockianus strain GE-1. Insights of the genome sequence and the methodologies that were applied during de novo assembly and annotation are given in detail. The finished genome shows a phred quality value of QV50. The complete genome size is 2.38 Mb, comprising the chromosome (2,035,182 bp), the megaplasmid pTB1 (342,792 bp) and the smaller plasmid pTB2 (10,299 bp). Gene prediction revealed 2,511 genes in total, including 2,458 protein-encoding genes, 53 RNA and 66 pseudo genes. A unique genomic region on megaplasmid pTB1 was identified encoding key enzymes for xylan depolymerization and xylose metabolism. This is in agreement with the growth experiments in which xylan is utilized as sole source of carbon. Accordingly, we identified sequences encoding the xylanase Xyn10, an endoglucanase, the membrane ABC sugar transporter XylH, the xylose-binding protein XylF, the xylose isomerase XylA catalyzing the first step of xylose metabolism and the xylulokinase XylB, responsible for the second step of xylose metabolism. Our data indicate that an ancestor of T. brockianus obtained the ability to use xylose as alternative carbon source by horizontal gene transfer.
KeywordsWhole genome sequence de novo assembly Thermus Thermus brockianus Xylan degradation Xylose metabolism Thermophiles Single molecule real-time sequencing
Members of the genus Thermus are Gram-negative, rod-shaped, non-sporulating, thermophilic aerobic bacteria. They have been discovered from various environments with elevated temperatures, including hot springs, deep-sea hot vents, volcanic eruptions and solfatara fields [1–4]. Thermus aquaticus was first isolated in 1969 in hot springs in Yellowstone National Park, USA . Thermus species and their produced enzymes, so called extremozymes, have attracted the attention of scientists from academia and industry due to their unique properties and metabolic pathways. Robust biocatalysts are attractive to various applications that often prevail in industrial processes [6–8]. The most prominent example of an industrial-relevant extremozyme is the DNA polymerase from T. aquaticus that is applied in polymerase chain reaction. Further industrial applications using enzymes from Thermus species include laundry detergents, DNA clean up prior to PCR or C-terminal sequencing [9–12]. Recently two glycoside hydrolases from T. antranikianii and T. brockianus were described and extended this group of industrial-relevant enzymes .
T. brockianus strain GE-1 was chosen for whole genome sequencing due to its ability to use xylan as sole carbon source and degrade xylan-rich substrates (Blank and Antranikian, unpublished results) . To our knowledge the hydrolysis of xylan has not been described for any other T. brockianus strain so far, including type strain YS038T . With the description of the corresponding thermostable xylanase, Xyn10, we already identified and characterized one of the key enzymes in a putative xylan degradation pathway of T. brockianus GE-1 . The identification and characterization of other polymer degrading enzymes from Thermus species is of great interest since there are only few reports regarding this aspect [16, 17]. Especially in the view of finding new solutions for global challenges like degradation of xenobiotic compounds or providing novel renewable energy sources, the xylanolytic behavior of T. brockianus GE-1 justifies further examination. These findings will also contribute to the development of biotechnological processes based on lignocellulose as carbon source (biorefinery). In this paper we present the first whole genome sequence of a T. brockianus strain with finished grade status, showing a phred quality value of QV50.
Classification and features
Classification and general features of T. brockianus GE-1 according to MIGS 
Species Thermus brockianus
pH range; Optimum
pH 7.0 – pH 8.0
Diverse set of sugars
Terrestrial hot springs
Geysir geothermal area, Iceland
Genome sequencing information
Genome project history
PacBio RS library
PacBio RS II
HGAP2 version 2.3.0
Gene calling method
CP016312, CP016313, CP016314
Genbank Date of Release
November 17, 2016
Source Material Identifier
Growth conditions and genomic DNA preparation
T. brockianus strain GE-1 was obtained from the strain culture collection of the Institute of Technical Microbiology at Hamburg University of Technology (TUHH). Deposition of the strain in the German National Culture Collection (DSMZ) is in progress. The strain was grown aerobically in DSMZ medium 878 ( Thermus 162 medium) at 70 °C for at least 48 h and agitation speed of 160 rpm . The genomic DNA of T. brockianus GE-1 was isolated using the PowerSoil DNA Isolation Kit (Mobio, USA). All steps were performed according to the manufacture’s instructions. Quality control of the isolated DNA was checked at GATC Biotech AG (Konstanz, Germany) prior to sequencing. A DNA concentration of 83.1 ng/μl and a 260/280 ratio of 1.87 were determined.
Genome sequencing and assembly
Third generation sequencing technology from Pacific Biosciences was chosen for whole de novo genome sequencing of T. brockianus strain GE-1 because its continuous long reads of up to 10 kb covering the longest known bacterial and archaeal repetitive regions and thus facilitate the generation of complete bacterial genome assemblies [21, 22]. Library construction, quantification and sequencing were performed at GATC Biotech AG (Konstanz, Germany). A Pacbio RS library (8–12 kb) was constructed and one SMRT cell was used for sequencing. 86,479 subreads were obtained after filtering and a total of 447.6 Mb with a N50 contig length of 2,058,948 bp were used for assembly. Pacific Biosciences sequencing data were assembled using an implemented version of PacBio SMRT Analysis, version 2.3.0 and the HGAP2 protocol (Pacific Biosciences, USA) . Minimum seed read length was automatically determined by the protocol with a length cut-off of 10,819 bp. The sum of contig lengths was 2,431,825 bp. The final de novo assembly obtained three circular contigs, providing the complete genome sequence of T. brockianus strain GE-1 and genome coverage of 156.56. Each contig represented one replicon, including the chromosome (2,035,182 bp), the megaplasmid pTB1 (342,792 bp) and plasmid pTB2 (10,299 bp). Circularization of each replicon was checked and performed by using circlator . Quality value of > QV50 (1 error probability in 100,000 base calls) for each replicon was reached after several polishing steps using the quiver algorithm, included in PacBio SMRT Analysis, version 2.3.0 .
Preliminary genome annotation was performed using the Prokka annotation pipeline v1.12 , followed by manual curation. Genes were identified by both Prodigal v2.6.3  and Glimmer v3.0.2 . Predicted coding sequences were translated and used to search the NCBI non-redundant database , UniProt  and Pfam  databases. The cmmscan and cmmsearch tools of the Hmmer3 package were used for protein similarity searches against HMM databases . For COG classification RPS-BLAST was used to search against the COG database . For rRNA detection we used RNAmmer v1.2 , while the tRNA prediction was performed by tRNAscan-SE v1.3.1 . Non-coding RNAs and regulatory RNA features were identified by searching the genome for corresponding Ram profiles using INFERNAL v1.1.1 . Signal peptides were identified by Signalp v4.1  and clustered regularly interspaced short palindromic repeats (CRISPR) were detected by using MinCED v0.2.0 included in the Prokka annotation pipeline . Analyses to identify genes that were assigned to transmembrane domains were performed by using tmhmm . Circular maps were created using CGView .
Summary of the genome of Thermus brockianus GE-1: 1 chromosome and 2 plasmids
% of Totala
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, Cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
Comparison of genomes from T. brockianus GE-1 and other Thermus species
Based on the availability of their finished genomes within the NCBI genome database we compare the T. brockianus GE-1 genome with six other Thermus species and seven genomes, including T. thermophilus HB8, T. thermophilus HB27 , T. scotoductus SA-01 , Thermus sp. CCB_US3_UF1 , T. oshimai JL-2 , T. aquaticus Y51MC23  and T. parvatiensis . With 2.38 Mb the genome of T. brockianus GE-1 is the largest one of these finished genomes, close to the genomes of T. oshimai JL-2 (2.33 Mb), T. aquaticus Y51MC23 (2.34 Mb) and T. scotoductus SA-01 (2.36 Mb) and much bigger than Thermus sp. CCB_US3_UF1 (2.26 Mb), T. thermophilus HB8 (2.12 Mb), T. thermophilus HB27 (2.13 Mb) and T. parvatiensis (2.03 Mb). All of those finished genomes include a chromosome and at least one plasmid. The genome of T. brockianus GE-1 consists of one chromosome (2.04 Mb) and two plasmids, including megaplasmid pTB1 (0.34 Mb) and plasmid pTB2 (10 kb). In number and size of those replicons the genome of T. brockianus GE-1 is similar to T. thermophilus HB8 having a chromosome (1.85 Mb), the megaplasmid pTT27 (0.26 Mb) and the plasmid pTT8 (9.3 kb) as well as T. oshimai JL-2 with one chromosome (2.07 Mb), one megaplasmid pTHEOS01 (0.27 Mb) and one plasmid pTHEOS02 (6 kb). Megaplasmids are a common feature of Thermus spp., since they were also identified in T. thermophilus HB27 (pTT27; 0.23 Mb) and T. parvatiensis (pTP143; 0.14 Mb). Due to their thermophilic lifestyle, all finished Thermus genomes exhibit a high GC content varying between 64.9% for T. scotoductus SA-01 and 69.5% for T. thermophilus HB8 with an average value of 67.0% GC content for the genome of T. brockianus GE-1.
With its total gene number of 2,511 and 2,458 protein-encoding genes, the genome of T. brockianus GE-1 showed high-ranking numbers in comparison to the available genomes, comparable to T. oshimai JL-2 (2,580 in total and 2,436 protein-encoding genes), T. scotoductus SA-1 (2,511 and 2,458), T. aquaticus Y51MC23 (2,484 and 2,325) and higher than Thermus sp. CCB_US3_UF1 (2,333 and 2,279), T. thermophilus HB8 (2,226 and 2,173), T. thermophilus HB27 (2,263 and 2,210) and T. parvatiensis (1,573 and 2,190). The genome of T. brockianus GE-1 encodes 47 tRNA genes and 6 rRNA genes, similar to most of the other finished genomes. Additionally, eight clustered regularly interspaced short palindromic repeats (CRISPRs) were identified in the genome of T. brockianus GE-1, suggesting the presence of a defense mechanism against phage DNA invasion, equivalent to other finished Thermus genomes with reported CRISPR sequences, including Thermus sp. CCB_US3_UF1 (8), T. thermophilus HB8 (11) and HB27 (10) and T. scotoductus SA-01 (3) .
By whole genome comparison analyses we identified the highest number of protein orthologs in the genomes of T oshimai (85.86%) and T. aquaticus (85.34%). These two genomes shared 2,156 and 2,143 of the 2,511 total proteins with T. brockianus GE-1. Further comparisons revealed 83.07% protein orthologs in comparison to Thermus sp. CCB_US3_UF1 (2,086 of 2,511), 82.44% to T. scotoductus (2,070 of 2,511), 81.96% to T. thermophilus HB8 (2,058 of 2,511) and 81.76% to T. thermophilus HB27 (2,053 of 2,511). With 1,661 and 66.15% we identified the lowest numbers of protein orthologs between T. parvatiensis and T. brockianus GE-1.
The number of total and protein-encoding genes on megaplasmid pTB1 were 314 and 299 as well as 13 for both in case of pTB2. Especially, the number of genes on the megaplasmid pTB1 is much higher compared to other available megaplasmids, since their total gene numbers vary between 150 (T. parvatiensis) and 251 ( T. thermophilus HB8). These differences are explicable by the smaller size of both megaplasmids (0.14 Mb for pTP143 and 0.26 MB for pTT27) in comparison to pTB1 (0.34 Mb). In contrast, the size of pTB2 (10 kb) is smaller than most other additional plasmids, which were reported to be 6–60 kb.
General metabolic pathways were investigated by KEGG analysis and revealed complete sets of genes for glycolysis, gluconeogenesis, citrate cycle, pentose phosphate pathway as well as genes involved in the lipid-, nucleotide-, amino acid-, cofactor- and vitamin-metabolism. For nutrient uptake, we identified 14 ABC transporters. All of these genes were localized on the chromosome of T. brockianus GE-1.
Xylan degradation pathway
Thermophilic bacteria like T. brockianus are of great industrial relevance, because they produce heat-stable and heat-active enzymes, so called thermozymes that perfectly match harsh process conditions. With regard to biocatalysts with a great potential for biotechnological processes, e.g. biorefinery, we identified sequences encoding putative lipases, subtilisin-like proteases, glucosidases and galactosidases in the genome of T. brockianus GE-1. The observed ability of this strain to degrade xylan-rich substrates and the identification of the responsible xylanase Xyn10 in our previous study directed our interest towards the investigation of the xylan degradation pathway by performing an analysis of the whole genome sequence of T. brockianus GE-1 . Interestingly, there is no homologue xylanase sequence detectable in any other Thermus genome that is currently available. Thus, the amino acid sequence of the xylanase Xyn10 from T. brockianus strain GE-1 displays the highest identity (57%) to a 1,4-β xylanase from Streptomyces sp. NRRL WC-3723. These two organisms are not closely related but it can be hypothesized that due to similar environmental conditions an ancestor of T. brockianus obtained the coding sequence of xyn10 by horizontal gene transfer. Another interesting fact to consider is that the localization of the corresponding gene xyn10 was not detected on the bacterial chromosome like other hydrolases, including lipases, peptidases and ATPases.
Thermus spp. and their extremozymes are of great interest for a wide set of industrial applications. Here we present the first whole genome sequence of T. brockianus GE-1, providing further insights into the biotechnological potential of the genus Thermus spp. in general and T. brockianus GE-1 specifically. The genome of T. brockianus GE-1 consists of a chromosome and two plasmids, including the megaplasmid pTB1. Sequences coding for essential metabolism pathways like glycolysis, gluconeogenesis, pentose phosphate pathway or citrate cycle were assigned to the bacterial chromosome just as well as sequences encoding industrial relevant enzymes, including galactosidases, glucosidases, lipases and subtilisin-like proteases. These novel extremozymes will be targets of prospective characterization studies to prove their industrial relevance. However, localization of gene xyn10 coding for a previously described xylanase from T. brockianus GE-1 was not detected on the chromosome but on the megaplasmid pTB1 adjacent to sequences encoding key enzymes for cellulose degradation and xylose metabolism. Thus, in accordance to a reported β-xylosidase side activity of xylanase Xyn10 the complete breakdown of xylan to D-xylose is genetically linked to the xylose metabolism in the genome of T. brockianus GE-1. These findings are consistent with the described xylanolytic activity of T. brockianus GE-1. The described combination of the identification of novel sequences encoding putative biocatalysts on the one hand and the description of a xylanolytic degradation pathway on the other hand emphasize the importance of Thermus spp. as promising sources of extremozymes with potential industrial value.
Clusters of Orthologous Groups
Clustered regularly interspaced short palindromic repeats
The authors thank Milton Simões da Costa for the kind gift of strain Thermus brockianus GE-1. We also thank Carola Schröder for discussion and critical reading of the manuscript. This publication was supported by the German Research Foundation (DFG) and the Hamburg University of Technology (TUHH) in the funding programme “Open Access Publishing”.
CS, SE and GA conceived and designed the analysis. CS performed the complete genome production, including genome assembly, annotation and GenBank submission. SB and SW prepared the DNA isolation and the cultivation of Thermus brockianus strain GE-1. SW performed the microscopic studies of Thermus brockianus strain GE-1. SE and CS worked on phylogenetics and pathway analyses. GA provided reagents and tools. CS drafted the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Antranikian G, Egorova K. Extremophiles, a unique source of biocatalysts for industrial biotechnology. In: Gerday C, Glansdorff N, editors. Physiology and Biochemistry of Extremophiles. ASM Press: Wahington D.C; 2007. p. 361–406.View ArticleGoogle Scholar
- Elleuche S, Schäfers C, Blank S, Schröder C, Antranikian G. Exploration of extremophiles for high temperature biotechnological processes. Curr Opin Microbiol. 2015;25:113–9.View ArticlePubMedGoogle Scholar
- Madigan MT, Marrs BL. Extremophiles. Sci Am. 1997;276:82–7.View ArticlePubMedGoogle Scholar
- Vieille C, Zeikus GJ. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev. 2001;65:1–43.View ArticlePubMedPubMed CentralGoogle Scholar
- Brock TD, Freeze H. Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol. 1969;98:289–97.PubMedPubMed CentralGoogle Scholar
- Schäfers C, Elleuche S, Antranikian G. Biochemical Properties and Applications of Heat-active Biocatalysts. In: Li F-L, editor. Thermophilic Microorganisms. Norfolk: Caister Academic Press; 2015. p. 47–90.View ArticleGoogle Scholar
- Cava F, Hidalgo A, Berenguer J. Thermus thermophilus as biological model. Extremophiles. 2009;13:213–31.View ArticlePubMedGoogle Scholar
- Sazanov LA, Hinchliffe P. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science. 2006;311:1430–6.View ArticlePubMedGoogle Scholar
- Matsuzawa H, Tokugawa K, Hamaoki M, Mizoguchi M, Taguchi H, Terada I, et al. Purification and characterization of aqualysin I (a thermophilic alkaline serine protease) produced by Thermus aquaticus YT-1. Eur J Biochem. 1988;171:441–7.View ArticlePubMedGoogle Scholar
- Bruins ME, Janssen AE, Boom RM. Thermozymes and their applications: a review of recent literature and patents. Appl Biochem Biotechnol. 2001;90:155–86.View ArticlePubMedGoogle Scholar
- Lee SH, Minagawa E, Taguchi H, Matsuzawa H, Ohta T, Kaminogawa S, et al. Purification and characterization of a thermostable carboxypeptidase (carboxypeptidase Taq) from Thermus aquaticus YT-1. Biosci Biotechnol Biochem. 1992;56:1839–44.View ArticlePubMedGoogle Scholar
- Minagawa E, Kaminogawa S, Matsuzawa H, Ohta T, Yamauchi K. Isolation and Characterization of a Thermostable Aminopeptidase (Aminopeptidase T) from Thermus aquaticus YT-1, an Extremely Thermophilic Bacterium (Biological Chemistry). Agric Biol Chem. 1988;52:1755–63.Google Scholar
- Schröder C, Blank S, Antranikian G. First Glycoside Hydrolase Family 2 Enzymes from Thermus antranikianii and Thermus brockianus with beta-Glucosidase Activity. Front Bioeng Biotechnol. 2015;3:76.PubMedPubMed CentralGoogle Scholar
- Blank S, Schröder C, Schirrmacher G, Reisinger C, Antranikian G. Biochemical characterization of a recombinant xylanase from Thermus brockianus, suitable for biofuel production. JSM Biotechnol Biomed Eng. 2014;2:1027.Google Scholar
- Chung AP, Rainey FA, Valente M, Nobre MF, da Costa MS. Thermus igniterrae sp. nov. and Thermus antranikianii sp. nov., two new species from Iceland. Int J Syst Evol Microbiol. 2000;50 Pt 1:209–17.
- Cordova LT, Lu J, Cipolla RM, Sandoval NR, Long CP, Antoniewicz MR. Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by (13)C metabolic flux analysis and whole genome sequencing. Metab Eng. 2016;37:63–71.View ArticlePubMedGoogle Scholar
- Lyon PF, Beffa T, Blanc M, Auling G, Aragno M. Isolation and characterization of highly thermophilic xylanolytic Thermus thermophilus strains from hot composts. Can J Microbiol. 2000;46:1029–35.View ArticlePubMedGoogle Scholar
- Huang XQ, Miller W. A Time-Efficient, Linear-Space Local Similarity Algorithm. Advances in Applied Mathematics. 1991;12:337–57.View ArticleGoogle Scholar
- Da Costa MS, Rainey FA, Nobre MF. The Genus Thermus and Relatives. In: Dworkin M, et al., Editors. The Prokaryotes: Volume 7: Proteobacteria: Delta, Epsilon Subclass. New York: Springer New York; 2006. p. 797-812.
- Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Treangen TJ, Abraham AL, Touchon M, Rocha EP. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev. 2009;33:539–71.View ArticlePubMedGoogle Scholar
- Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10:563–9.View ArticlePubMedGoogle Scholar
- Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 2015;16:294.View ArticlePubMedPubMed CentralGoogle Scholar
- Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.View ArticlePubMedGoogle Scholar
- Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.View ArticlePubMedPubMed CentralGoogle Scholar
- Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23:673–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Altschul SF, Gish W. Local alignment statistics. Methods Enzymol. 1996;266:460–80.View ArticlePubMedGoogle Scholar
- Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, et al. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2004;32:D115–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44:D279–85.View ArticlePubMedGoogle Scholar
- Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755–63.View ArticlePubMedGoogle Scholar
- Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011;39:D225–9.View ArticlePubMedGoogle Scholar
- Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100–8.View ArticlePubMedPubMed CentralGoogle Scholar
- Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.View ArticlePubMedPubMed CentralGoogle Scholar
- Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009;25:1335–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–6.View ArticlePubMedGoogle Scholar
- Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007;8:209.View ArticlePubMedPubMed CentralGoogle Scholar
- Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.View ArticlePubMedGoogle Scholar
- Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics. 2005;21:537–9.View ArticlePubMedGoogle Scholar
- Henne A, Brüggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, et al. The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol. 2004;22:547–53.View ArticlePubMedGoogle Scholar
- Gounder K, Brzuszkiewicz E, Liesegang H, Wollherr A, Daniel R, Gottschalk G, et al. Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. BMC Genomics. 2011;12:577.View ArticlePubMedPubMed CentralGoogle Scholar
- Teh BS, Lau NS, Ng FL, Abdul Rahman AY, Wan X, Saito JA. Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. Stand Genomic Sci. 2015;10:76.View ArticlePubMedPubMed CentralGoogle Scholar
- Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han CS, et al. Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin. Genome Announc. 2013;1.
- Brumm PJ, Monsma S, Keough B, Jasinovica S, Ferguson E, Schoenfeld T, et al. Complete Genome Sequence of Thermus aquaticus Y51MC23. PLoS One. 2015;10, e0138674.View ArticlePubMedPubMed CentralGoogle Scholar
- Dwivedi V, Sangwan N, Nigam A, Garg N, Niharika N, Khurana P, et al. Draft genome sequence of Thermus sp. strain RL, isolated from a hot water spring located atop the Himalayan ranges at Manikaran, India. J Bacteriol. 2012;194:3534.View ArticlePubMedPubMed CentralGoogle Scholar
- Biely P. Microbial Xylanolytic Systems Trends in Biotechnology. 1985;3:286–90.Google Scholar
- Wu YW, Joshua C, Eichorst SA, Gladden JM, Simmons BA, Singer SW. Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia. Bioenergy Res. 2015;8:1031–8.View ArticleGoogle Scholar
- Ohtani N, Tomita M, Itaya M. The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination. Extremophiles. 2012;16:237–44.View ArticlePubMedGoogle Scholar
- Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Skerman VBD, Mcgowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980;30:225–420.View ArticleGoogle Scholar
- Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol. 1989;11:128–34.View ArticlePubMedGoogle Scholar
- Garrity GM. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol. 2005;55:2235–8.View ArticleGoogle Scholar
- Garrity GM, Holt JG. Class I. Deinococci class. nov. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s Manual of Systematic Bacteriology, vol. 1. 2nd ed. New York: Springer; 2001. p. 395.View ArticleGoogle Scholar
- Rainey FA, da Costa MS. Thermalesord. nov. Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Ltd.; 2015. doi:10.1002/9781118960608.obm00045.
- Da Costa M, Rainey F, Family I. Thermaceae fam. nov. Bergey's Manual of Systematic Bacteriology. 2001;1:403–4.Google Scholar
- Nobre MF, Trüper HG, da Costa MS. 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. Int J Syst Evol Microbiol. 1999;49:1951–1.
- Williams RA, Smith KE, Welch SG, Micallef J, Sharp RJ. DNA relatedness of Thermus strains, description of Thermus brockianus sp. nov., and proposal to reestablish Thermus thermophilus (Oshima and Imahori). Int J Syst Bacteriol. 1995;45:495–9.View ArticlePubMedGoogle Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat Genet. 2000;25:25–9.PubMedGoogle Scholar
- Felsenstein J. PHYLIP: phylogenetic inference package [3.6]. Seattle, WA: University of Washington; 1991.Google Scholar
- Page RD. Visualizing phylogenetic trees using TreeView. Curr Protoc Bioinformatics, 2002;Chapter 6:Unit 6 2.
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0.. Bioinformatics. 2007;23:2947–8.View ArticlePubMedGoogle Scholar