Volume 8, Number 11—November 2002
Genomewide Pattern of Synonymous Nucleotide Substitution in Two Complete Genomes of Mycobacterium tuberculosis
|Reference||No. loci||Synomymous substitutions/site/yr||Divergence time (H37Rv and CDC1551)|
|11||67||4.7 ± 0.2 X 10-9||34,900 ± 2,300 b (33,500–36,400) c|
|12||128||4.4 X 10-9||37,300 ± 2,500 b|
- Kato-Maeda M, Bifani PJ, Kreiswirth BN, Small PN. The nature and consequence of genetic diversity within Mycobacterium tuberculosis. J Clin Invest. 2001;107:533–7.
- Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent dissemination. Proc Natl Acad Sci U S A. 1997;94:9869–74.
- Kapur V, Whittam TS, Musser JM. Is Mycobacterium tuberculosis 15,000 years old? J Infect Dis. 1994;170:1348–9.
- Betts JC, Dodson P, Quan S, Lewis AP, Thomas PJ, Duncan K, Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology. 2000;146:3205–16.
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.
- Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673–80.
- Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986;3:418–26.
- Hughes AL. Adaptive evolution of genes and genomes. New York: Oxford University Press; 1999.
- The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001;409:928–33.
- Ochman H, Elwyn S, Moran NA. Calibrating bacterial evolution. Proc Natl Acad Sci U S A. 1999;96:12638–43.
- Sharp PM. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol. 1991;33:23–33.
- Smith NGC, Eyre-Walker A. Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions. Mol Biol Evol. 2001;18:2124–6.
- Ochman H, Wilson AC. Evolution in bacteria: evidence for a universal substitution rate in cellular organisms. J Mol Evol. 1987;26:74–86.
- Doolittle RF, Feng D-F, Tsang S, Cho G, Little E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science. 1996;271:470–7.
- Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393:537–44.
- Takahata N, Nei M. Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics. 1990;124:967–78.
- Le Dantec C, Winter N, Gicquel B, Vincent V, Picardeau P. Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems. J Bacteriol. 2001;183:2157–64.
- Stead WW. The origin and erratic global spread of tuberculosis. How the past explains the present and is the key to the future. Clin Chest Med. 1997;18:65–77.
- Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A. 2002;99:3684–9.
- Hughes AL, Verra F. Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum. Proc R Soc Lond B Biol Sci. 2001;268:1855–60.
- Mu J, Duan J, Makova KD, Joy DA, Huynh CQ, Branch OH, Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature. 2002;418:323–6.
- Burnet M. Natural history of infectious disease. Cambridge: Cambridge University Press; 1940.
- Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, Jiang L, Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science. 2002;296:2028–33.
- Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, Sequencing of the M. tuberculosis genome: comparison of a recent clinical isolate with the laboratory strain. J Bacteriol. 2002. In press.
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