Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Case Reports
. 2017 Oct 11:12:62.
doi: 10.1186/s40793-017-0271-1. eCollection 2017.

Complete genome sequence of Thermotoga sp. strain RQ7

Zhaohui Xu  1 , Rutika Puranik  1 , Junxi Hu  1   2 , Hui Xu  1 , Dongmei Han  1
Affiliations
Case Reports

Complete genome sequence of Thermotoga sp. strain RQ7

Zhaohui Xu et al. Stand Genomic Sci. .

Abstract

Thermotoga sp. strain RQ7 is a member of the family Thermotogaceae in the order Thermotogales. It is a Gram negative, hyperthermophilic, and strictly anaerobic bacterium. It grows on diverse simple and complex carbohydrates and can use protons as the final electron acceptor. Its complete genome is composed of a chromosome of 1,851,618 bp and a plasmid of 846 bp. The chromosome contains 1906 putative genes, including 1853 protein coding genes and 53 RNA genes. The genetic features pertaining to various lateral gene transfer mechanisms are analyzed. The genome carries a complete set of putative competence genes, 8 loci of CRISPRs, and a deletion of a well-conserved Type II R-M system.

Keywords: CP007633; CRISPR; Natural competence; Restriction-modification system; T. sp. strain RQ7; Thermotoga; TneDI.

PubMed Disclaimer

Conflict of interest statement

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Phylogenetic tree showing the position of T. sp. strain RQ7 relative to other species within the order Thermotogales. Only species with complete genome sequences are included. The tree was built with 16S rRNA gene sequences, using the Neighbor-Joining method with MEGA7 [50]. Fervidobacterium nodosum serves as the outgroup
Fig. 2
Fig. 2
Scanning electron micrograph of T. sp. strain RQ7 cells after 12 h of growth. Bar, 0.5 μm
Fig. 3
Fig. 3
Chromosomal map of T. sp. strain RQ7. From outside to the center: genes on forward strand (color by COG categories), genes on reverse strand (color by COG categories), RNA genes (tRNAs: green, rRNAs: red, other RNAs: black), GC content (black), GC skew (olive/purple)
Fig. 4
Fig. 4
Full genome alignment of the four Thermotoga strains using Mauve [53]. Each horizontal panel represents one genome sequence, from top to bottom: T. neapolitana DSM 4359, T. sp. strain RQ7, T. sp. strain RQ2, and T. maritima MSB8. The sequences were downloaded from GenBank, and genomes of T. neapolitana DSM 4359 and T. maritima MSB8 were re-linearized at the dnaA gene. Blocks with the same color represent homologous regions. Blocks below the center lines are inversed regions. Inside of each block, the height of the similarity profile corresponds to the average level of conservation of the local area
Fig. 5
Fig. 5
Diagrammatic representation of CRISPR/Cas systems in T. sp. strain RQ7. a Positions of the 8 regions of CRISPR arrays; drawn in scale using Clone Manager Professional Suite v.8 [82]. b Positions of the cas genes (open boxed) relative to the CRISPR arrays (filled boxes); not in scale
Fig. 6
Fig. 6
Deletion of the TneDI system in T. sp. RQ7. The neighborhoods of the deletion site were compared (color by COG categories). The big rectangle box highlights the R-M system that is absent in T. sp. strain RQ7 (show as RQ7 in the diagram). The numerical values are genome coordinates as documented in JGI-IMG. RQ2, T. sp. strain RQ2; Tm, T. maritima MSB8; Tn, T. neapolitana DSM 4359
Fig. 7
Fig. 7
Experimental confirmation of the deletion of the TneDI system in T. sp. strain RQ7. T. neapolitana DSM 4359 (Tn) was used as the positive control. The expected sizes are 1831 bp in T. neapolitana DSM 4359 and 503 bp in T. sp. strain RQ7
Fig. 8
Fig. 8
Digestion of the genomic DNA of T. neapolitana DSM 4359 (Tn), T. sp. strain RQ2 (RQ2), T. maritima MSB8 (Tm), and T. sp. strain RQ7 (RQ7) with R.TneDI. -, negative control, no R.TneDI; +, digestion with R.TneDI; m_+, DNA was treated with M.TneDI prior to being digested by R.TneDI
Fig. 9
Fig. 9
Digestion of genomic DNA of T. maritima MSB8 (Tm), T. neapolitana DSM 4359 (Tn), T. sp. strain RQ2 (RQ2), and T. sp. strain RQ7 by BstUI. -, negative control, no BstUI; +, treated with BstUI
See this image and copyright information in PMC

References

    1. Huber R, Langworthy TA, Konig H, Thomm M, Woese CR, Sleytr UB, Stetter KO. Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90 degrees C. Arch Microbiol. 1986;144(4):324–333. doi: 10.1007/BF00409880. - DOI
    1. Schroder C, Selig M, Schonheit P. Glucose Fermentation to Acetate, CO2 and H2 in the Anaerobic Hyperthermophilic Eubacterium Thermotoga Maritima: Involvement of the Embden-Meyerhof Pathway. Arch Microbiol. 1994;161(6):460–470.
    1. Takahata Y, Nishijima M, Hoaki T, petrophila MTT. sp. nov. and Thermotoga naphthophila sp. nov., two hyperthermophilic bacteria from the Kubiki oil reservoir in Niigata, Japan. Int J Syst Evol Microbiol. 2001;51:1901–1909. doi: 10.1099/00207713-51-5-1901. - DOI - PubMed
    1. Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbo CL, Doolittle WF, Gogarten JP, et al. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci U S A. 2009;106(14):5865–5870. doi: 10.1073/pnas.0901260106. - DOI - PMC - PubMed
    1. Nesbo CL, Dlutek M, Doolittle WF. Recombination in thermotoga: Implications for species concepts and biogeography. Genetics. 2006;172(2):759–769. doi: 10.1534/genetics.105.049312. - DOI - PMC - PubMed

Publication types

LinkOut - more resources