Comparative genomics and understanding of microbial biology.

The sequences of close to 30 microbial genomes have been completed during the past 5 years, and the sequences of more than 100 genomes should be completed in the next 2 to 4 years. Soon, completed microbial genome sequences will represent a collection of >200,000 predicted coding sequences. While analysis of a single genome provides tremendous biological insights on any given organism, comparative analysis of multiple genomes provides substantially more information on the physiology and evolution of microbial species and expands our ability to better assign putative function to predicted coding sequences.

[1]  H. Ochman,et al.  Molecular archaeology of the Escherichia coli genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  P. Haslett,et al.  Mycobacterium tuberculosis CDC1551 induces a more vigorous host response in vivo and in vitro, but is not more virulent than other clinical isolates. , 1999, Journal of immunology.

[3]  Y. Kawarabayasi,et al.  Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. , 1999, DNA research : an international journal for rapid publication of reports on genes and genomes.

[4]  S. Salzberg,et al.  Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. , 1999, Science.

[5]  E V Koonin,et al.  Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. , 1998, Science.

[6]  R. Fleischmann,et al.  The Minimal Gene Complement of Mycoplasma genitalium , 1995, Science.

[7]  R. Gwilliam,et al.  The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum , 1999, Nature.

[8]  C R Woese,et al.  Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1998, Nature.

[9]  J A Eisen,et al.  Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. , 1998, Genome research.

[10]  T. Whittam,et al.  Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Mark Borodovsky,et al.  The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.

[12]  S. Razin Molecular biology and genetics of mycoplasmas (Mollicutes) , 1985, Microbiological reviews.

[13]  S. Sunkin,et al.  Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[14]  P. Hanawalt,et al.  A phylogenomic study of DNA repair genes, proteins, and processes. , 1999, Mutation research.

[15]  R. Huber,et al.  The complete genome of the hyperthermophilic bacterium Aquifex aeolicus , 1998, Nature.

[16]  R. Quatrano Genomics , 1998, Plant Cell.

[17]  W. Doolittle,et al.  Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S. Salzberg,et al.  Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. , 2000, Science.

[19]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[20]  J. L. Montagne,et al.  Emerging infectious diseases. , 1994, The Journal of infectious diseases.

[21]  B. Barrell,et al.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.

[22]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[23]  B. Barrell,et al.  The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences , 2000, Nature.

[24]  André Goffeau,et al.  The yeast genome directory. , 1997, Nature.

[25]  J A Eisen,et al.  A phylogenomic study of the MutS family of proteins. , 1998, Nucleic acids research.

[26]  J. Felsenstein Phylogenies and the Comparative Method , 1985, The American Naturalist.

[27]  Sayaka,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[28]  S. Salzberg,et al.  Complete genome sequence of Treponema pallidum, the syphilis spirochete. , 1998, Science.

[29]  S. Salzberg,et al.  Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi , 1997, Nature.

[30]  O. White,et al.  A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi , 2000, Molecular microbiology.

[31]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[32]  F. Robb,et al.  Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.

[33]  S. Salzberg,et al.  Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. , 2000, Nucleic acids research.

[34]  M. Gouy,et al.  A nonhyperthermophilic common ancestor to extant life forms. , 1999, Science.

[35]  R. W. Davis,et al.  Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. , 1998, Science.

[36]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[37]  R. Fleischmann,et al.  Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii , 1996, Science.

[38]  Ronald W. Davis,et al.  Comparative genomes of Chlamydia pneumoniae and C. trachomatis , 1999, Nature Genetics.

[39]  R. Fleischmann,et al.  The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1997, Nature.

[40]  Y. Nakamura,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement). , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[41]  A. Goffeau,et al.  The complete genome sequence of the Gram-positive bacterium Bacillus subtilis , 1997, Nature.

[42]  T. Sicheritz-Pontén,et al.  The genome sequence of Rickettsia prowazekii and the origin of mitochondria , 1998, Nature.

[43]  H. Hilbert,et al.  Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. , 1996, Nucleic acids research.

[44]  B. Barrell,et al.  Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491 , 2000, Nature.

[45]  Benjamin L. King,et al.  Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori , 1999, Nature.

[46]  S. Salzberg,et al.  Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima , 1999, Nature.

[47]  C. Hutchison,et al.  Characterization of repetitive DNA in the Mycoplasma genitalium genome: possible role in the generation of antigenic variation. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[48]  G. Church,et al.  Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics , 1997, Journal of bacteriology.