Microbial genomes: dealing with diversity

Alm, 1999, Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori, Nature, 397, 176, 10.1038/16495 Alm, 1999, Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes, J Mol Med, 77, 834, 10.1007/s001099900067 Stephens, 1998, Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis, Science, 282, 754, 10.1126/science.282.5389.754 Read, 2000, Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39, Nucleic Acids Res, 28, 1397, 10.1093/nar/28.6.1397 Kalman, 1999, Comparative genomes of Chlamydia pneumoniae and C. trachomatis, Nat Genet, 21, 385, 10.1038/7716 Tettelin, 2000, Complete genome sequence of Neisseria meningitidis serogroup B strain MC58, Science, 287, 1809, 10.1126/science.287.5459.1809 Parkhill, 2000, Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491, Nature, 404, 502, 10.1038/35006655 Lan, 2000, Intraspecies variation in bacterial genomes: the need for a species genome concept, Trends Microbiol, 8, 396, 10.1016/S0966-842X(00)01791-1 Takami, 2000, Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis, Nucleic Acids Res, 28, 4317, 10.1093/nar/28.21.4317 Maeder, 1999, Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences, Genetics, 152, 1299, 10.1093/genetics/152.4.1299 Diruggiero, 2000, Evidence of recent lateral gene transfer among hyperthermophilic archaea, Mol Microbiol, 38, 684, 10.1046/j.1365-2958.2000.02161.x McClelland, 2000, Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi, Nucleic Acids Res, 28, 4974, 10.1093/nar/28.24.4974 Behr, 1999, Comparative genomics of BCG vaccines by whole-genome DNA microarray, Science, 284, 1520, 10.1126/science.284.5419.1520 Salamon, 2000, Detection of deleted genomic DNA using a semiautomated computational analysis of gene chip data, Genome Res, 10, 2044, 10.1101/gr.GR-1529R Salama, 2000, A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains, Proc Natl Acad Sci USA, 97, 14668, 10.1073/pnas.97.26.14668 Ochman, 2000, Evolutionary dynamics of full genome content in Escherichia coli, EMBO J, 19, 6637, 10.1093/emboj/19.24.6637 Lan, 1996, Gene transfer is a major factor in bacterial evolution, Mol Biol Evol, 13, 47, 10.1093/oxfordjournals.molbev.a025569 Akopyants, 1998, PCR-based subtractive hybridization and differences in gene strains of Helicobacter pylori, Proc Natl Acad Sci USA, 95, 13108, 10.1073/pnas.95.22.13108 Lai, 2000, Identification of genes present specifically in a virulent strain of Klebsiella pneumoniae, Infect Immun, 68, 7149, 10.1128/IAI.68.12.7149-7151.2000 Bogush, 1999, Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization, Mol Gen Genet, 262, 721, 10.1007/s004380051134 Ochman, 2000, Lateral gene transfer and the nature of bacterial innovation, Nature, 405, 299, 10.1038/35012500 Woese, 2000, Interpreting the universal phylogenetic tree, Proc Natl Acad Sci USA, 97, 8392, 10.1073/pnas.97.15.8392 Jain, 1999, Horizontal gene transfer among genomes: the complexity hypothesis, Proc Natl Acad Sci USA, 96, 3801, 10.1073/pnas.96.7.3801 Woese, 2000, Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process, Microbiol Mol Biol Rev, 64, 202, 10.1128/MMBR.64.1.202-236.2000 Brochier, 2000, The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome, Trends Genet, 16, 529, 10.1016/S0168-9525(00)02142-9 Hansmann, 2000, Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis, Int J Syst Evol Micro, 50, 1655, 10.1099/00207713-50-4-1655 Ke, 2000, Evidence for horizontal gene transfer in evolution of elongation factor Tu in enterococci, J Bacteriol, 182, 6913, 10.1128/JB.182.24.6913-6920.2000 Yap, 1999, Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon, J Bacteriol, 181, 5201, 10.1128/JB.181.17.5201-5209.1999 Ueda, 1999, Two distinct mechanisms cause heterogeneity of 16S rRNA, J Bacteriol, 181, 78, 10.1128/JB.181.1.78-82.1999 Anton, 1999, Intraspecific diversity of the 23S rRNA gene and the space region downstream in Escherichia coli, J Bacteriol, 181, 2703, 10.1128/JB.181.9.2703-2709.1999 Dennis, 1998, Transcription analysis of two disparate rRNA operons in the halophilic archaeon Haloarcula marismortui, J Bacteriol, 180, 4804, 10.1128/JB.180.18.4804-4813.1998 Amann, 2000, Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui, Extremophiles, 4, 373, 10.1007/s007920070007 Kurland, 2000, Something for everyone: horizontal gene transfer in evolution, EMBO Reports, 1, 1, 10.1093/embo-reports/kvd042 Beja, 2000, Bacterial rhodopsin: evidence for a new type of phototrophy in the sea, Science, 289, 1902, 10.1126/science.289.5486.1902 Beja O., Suzuki M.T., Koonin E.V., Aravind L., Hadd A., Nguyen L.P., Villacorta R., Amjadi M., Garrigues, Jovanovich S.B. et al.: Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Mol Microbiol 2000, 2:516-529.This is a key paper in the birth of ‘culture-independent genomics’, which will, we predict, come to supplant current approaches. Perna, 2001, Genome sequence of enterohaemorrhagic Escherichia coli O157:H7, Nature, 409, 529, 10.1038/35054089