Abstract
We report the completely annotated genome sequence of Mycobacterium tuberculosis Erdman (TMC 107; ATCC 35801), which is a well-known laboratory strain of M. tuberculosis.
GENOME ANNOUNCEMENT
Mcobacterium tuberculosis strain Erdman was isolated from human sputum by William H. Feldman in 1945, at Mayo Clinic, Rochester, MN, and deposited with the Trudeau Mycobacterium Culture Collection in 1946 (7). There is no description of the naming of “Erdman” in reference 7. Due to its consistently high virulence (7), it has been widely used as a standard virulent laboratory strain for virulence and immunization studies. M. tuberculosis Erdman has a faster in vivo doubling time than two attenuated strains, M. tuberculosis H37Ra and Mycobacterium bovis Bacillus Calmette-Guerin (BCG), and a slightly faster in vivo doubling time than the virulent H37Rv strain in mice (5). The M. tuberculosis Erdman strain showed the same level of virulence as M. tuberculosis CDC1551 in C57BL/6 mice (2). We recently found that strain Erdman was quite virulent compared with a clinical isolate, M. tuberculosis NCGM2209 (4), in BALB/c mice (strain Erdman 50% lethal dose [LD50], 1 × 103/mouse; strain NCGM2209 LD50, >2 × 107/mouse) (data not shown; estimated from 180-day-mortality data by the method of Reed and Muench [6]).
First, the M. tuberculosis Erdman genome was analyzed using a GS FLX Titanium sequencer (Roche) with an 8-kb pair-end library prepared from the genome. This generated 976,847 reads, covering 358,569,827 bp, which were assembled into scaffolds and contigs by GS De Novo Assembler 2.6 (Newbler; Roche). Then, gap filling was performed using conventional Sanger sequencing of the PCR fragments, brute-force PCR for the contigs and scaffolds, and an ABI 3730xl DNA sequencer. Finally, 1,274,470-kb single-end reads obtained with Genome Analyzer IIx (Illumina) were used to add to the draft genome sequence by the use of Maq software (3). Primary coding sequence extractions and initial function assignments were performed using the automated annotation server RAST (Rapid Annotation using Subsystem Technology) (1). The results were compared to verify the annotation and were corrected manually by in silico molecular cloning (In Silico Biology Inc., Kanagawa, Japan). The M. tuberculosis Erdman genome consists of a single circular chromosome of 4,392,353 bp, with an average GC content of 65.6%. The chromosome was shown to contain a total of 4,246 protein-coding genes, 52 tRNA genes, one transfer mRNA for all amino acids, and 1 rrn operon. In addition, the chromosome harbors 11 IS6110 sequences.
Nucleotide sequence accession number.
Nucleotide sequences of the chromosome of M. tuberculosis Erdman have been deposited in the DNA Database of Japan under accession no. AP012340.
ACKNOWLEDGMENTS
This study was supported by Health Sciences Research grants (H21-SHINKO-IPPAN-016). T.K. and T.M.-A. were supported by Grants for International Health Research from the Ministry of Health, Labor, and Welfare of Japan (21A-6 and 23A-301, respectively). We thank N. Saito, S. Suzuki, and Y. Sakurai for their excellent work in the genome analysis.
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