No abstract

No abstract

No abstract

No abstract

A draft genome sequence of Tsukamurella sp., an aerobic bacterium isolated from a human sputum specimen, is described here. A new virus or provirus, TPA4, was characterized.T he genus Tsukamurella includes Gram-positive rods isolated from sludge foams, arthropods, soil, and in opportunistic clinical infections. Tsukamurella sp. strain 1534 was isolated from a human sputum specimen. Recently, the whole genome of Tsukamurella paurometabola was published (9).Both a shotgun sequencing and 3-kb paired-end sequencing were performed. The shotgun library was constructed with the GS Rapid library Prep kit (Roche). The library was constructed according to the 454 GS FLX Titanium paired-end protocol. The run was analyzed on the cluster through the GS RunBrowser and Newbler assembler 2.5.3. A total of 482,748 passed filter wells were obtained from the both strategies and generated 168.2 Mb with an average length of 348.5 bp. The draft genome of Tsukamurella sp. strain 1534 (about 4.5 Mb) contains 4 scaffolds and 42 large contigs (Ͼ1,500 bp). One other contig had a size of 935 bp.The GϩC content was 71.1%. The genome contains 54 tRNA genes and encodes 4,400 putative proteins. Of the coding sequences, 89.4% could be assigned to Cluster of Orthologous Groups (COG) families. The sequences of the rRNAs were found in one contig, but its average coverage was 55ϫ, compared with 37ϫ for the average coverage of the whole genome. It was therefore possible to conclude that probably 2 ribosomal operons were present. Open reading frames (ORFs) were predicted using Prodigal (http://prodigal.ornl.gov/) with default parameters but the predicted ORFs were excluded if they were spanning a sequencing gap region. The predicted bacterial protein sequences were searched against the National Center for Biotechnology Information (NCBI) Nonredundant (NR), UNIPROT (7), and CharProtDB (6) databases using BLASTP and the Clusters of Orthologous Groups (COG) (11) database using RPSBLAST (1). The ARAGORN tool (5) was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer (4) and BLASTn against the NR database.Reciprocal best BLAST analysis with the available genome of Tsukamurella paurometabola indicated that they shared 3,037 orthologs.Bacteriophages were described in other Tsukamurella spp., and the PHAST server (12) and Prophage Finder (2) were used to identify potential proviruses in Tsukamurella sp. strain 1534 genome. The bacterium contains one genetic element of around 49.4 kb (with a GϩC content of 70.1%) related to a virus named TPA4.