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J Bacteriol. 2012 March; 194(5): 1240.
PMCID: PMC3294796

Complete Genome Sequence of the Thermophilic Bacterium Thermus sp. Strain CCB_US3_UF1


Thermus sp. strain CCB_US3_UF1, a thermophilic bacterium, has been isolated from a hot spring in Malaysia. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1.


Thermus spp. are Gram-negative, aerobic, nonsporulating, and rod-shaped thermophilic bacteria (3). Members of the genus Thermus have potential in biotechnological applications as sources of thermostable DNA polymerase used in PCR techniques (10, 11). Here, we report the complete genome sequence of Thermus sp. strain CCB_US3_UF1, isolated from a hot spring in Ulu Slim, Perak, Malaysia, at 92.4°C, pH 7.

The genomic DNA of Thermus sp. CCB_US3_UF1 was extracted using a modified phenol-chloroform protocol (5). The whole-genome sequencing of Thermus sp. CCB_US3_UF1 was performed using Roche 454 and Solexa paired-end sequencing technology. A 3-kb genomic library was constructed, and 97,991 paired-end reads and 54,397 single-end reads were generated using the GS FLX system, providing 21.14-fold genome coverage. A total of 3,469,788 reads from the 3-kb library were produced to reach a depth of 115-fold coverage with an Illumina Solexa GA IIx (Illumina, San Diego, CA). These reads were mapped to the scaffolds using the Burrows-Wheeler alignment (BWA) tool (7).

The complete genome of Thermus sp. CCB_US3_UF1 is composed of a single circular chromosome of 2,243,772 bp and a plasmid of 19,716 bp, with G+C contents of 68.6% and 65.6%, respectively. There are 2,247 predicted coding sequences (CDS), 2 rRNA operons, and 48 tRNA genes. There are 32 predicted CDS in the plasmid. The automated annotation of the genome was done using the DIYA (Do-It-Yourself Annotator) pipeline (12). Open reading frames (ORFs) were identified using Glimmer3 (4), followed by a protein similarity search using BLAST (1) against UNIREF (13), RPS-BLAST against CDD (9), and Asgard (2). Transfer RNAs were predicted by using tRNAscan-SE (8), while ribosomal RNAs were identified by using RNAmmer (6).

The genome reveals that Thermus sp. CCB_US3_UF1 possesses numerous transporters for efficient substrate and nutrient uptake and for utilization of various energy sources.

Nucleotide sequence accession numbers.

The genome sequences of Thermus sp. CCB_US3_UF1 have been deposited in GenBank under accession numbers CP003126 (chromosome) and CP003127 (plasmid).


This work was supported by APEX funding (Malaysia Ministry of Higher Education) to the Centre for Chemical Biology, Universiti Sains Malaysia.


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