Assessing evolutionary relationships among microbes from whole-genome analysis.

The determination and analysis of complete genome sequences have recently enabled many major advances to be made in the area of microbial evolutionary biology. These include the determination of the first genome of a Crenarchaeota, the suggestion that horizontal gene transfer may be the rule rather than the exception, and revelations about how genomes evolve on short timescales.

[1]  S. Karlin,et al.  Dinucleotide relative abundance extremes: a genomic signature. , 1995, Trends in genetics : TIG.

[2]  J. Andersson,et al.  Genome degradation is an ongoing process in Rickettsia. , 1999, Molecular biology and evolution.

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

[4]  P. Forterre,et al.  The Rooting of the Universal Tree of Life Is Not Reliable , 1999, Journal of Molecular Evolution.

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

[6]  J. Lake,et al.  Horizontal gene transfer among genomes: the complexity hypothesis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[7]  E V Koonin,et al.  Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. , 1998, Trends in genetics : TIG.

[8]  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.

[9]  B. Snel,et al.  Genome phylogeny based on gene content , 1999, Nature Genetics.

[10]  S Brunak,et al.  Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. , 2000, Nucleic acids research.

[11]  L. Pauling,et al.  Molecules as documents of evolutionary history. , 1965, Journal of theoretical biology.

[12]  C. Woese,et al.  Bacterial evolution , 1987, Microbiological reviews.

[13]  M. Tomita,et al.  Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. , 1999, Nucleic acids research.

[14]  S. Karlin,et al.  Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[15]  W. Martin.  Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[16]  J. Andersson,et al.  Insights into the evolutionary process of genome degradation. , 1999, Current opinion in genetics & development.

[17]  W. Martin,et al.  The genome of Rickettsia prowazekii and some thoughts on the origin of mitochondria and hydrogenosomes. , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

[19]  C. Kurland,et al.  Origins of mitochondria and hydrogenosomes. , 1999, Current opinion in microbiology.

[20]  B. Dujon,et al.  The genomic tree as revealed from whole proteome comparisons. , 1999, Genome research.

[21]  C. Woese,et al.  Phylogenetic structure of the prokaryotic domain: The primary kingdoms , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[22]  S. Salzberg,et al.  DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae , 2000, Nature.

[23]  S. Fitz-Gibbon,et al.  Whole genome-based phylogenetic analysis of free-living microorganisms. , 1999, Nucleic acids research.

[24]  Eugen C. Buehler,et al.  Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana , 1999, Nature.

[25]  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.

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

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

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

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

[30]  C R Woese,et al.  An archaeal genomic signature. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[31]  C. Squires,et al.  An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

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

[33]  Doolittle Wf.  Phylogenetic Classification and the Universal Tree , 1999 .

[34]  William C. Nierman,et al.  Lin, X. et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768 , 1999 .

[35]  Michael Y. Galperin,et al.  Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. , 1999, Genome research.

[36]  S. Karlin,et al.  A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[38]  J. DiRuggiero,et al.  Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. , 1999, Genetics.

[39]  A EisenJ,et al.  DNA修復遺伝子,タンパクと過程のphylogenomic(系統発生的ゲノム)調査 , 1999 .

[40]  J. Logsdon,et al.  Thermotoga heats up lateral gene transfer. , 1999, Current biology : CB.

[41]  G. Olsen,et al.  Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? , 1999, Trends in genetics : TIG.

[42]  P. Sharp,et al.  Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. , 1999, Nucleic acids research.

[43]  H. Philippe,et al.  Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. , 1999, Molecular biology and evolution.

[44]  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.

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

[46]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

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

[48]  H. Ochman,et al.  Amelioration of Bacterial Genomes: Rates of Change and Exchange , 1997, Journal of Molecular Evolution.

[49]  L. Orgel,et al.  Phylogenetic Classification and the Universal Tree , 1999 .