1887

Abstract

There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple genomes has led to an estimate of around 45 000 gene families — more genes than are recognized in the human genome. Moreover, of the 1000 genomes available, not a single protein is conserved across all genomes. Excluding the members of the , only a total of four genes are conserved in all bacteria: two protein genes and two RNA genes.

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2010-03-01
2024-03-29
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References

  1. Ansorge W. J. 2009; Next-generation DNA sequencing techniques. Nat Biotechnol 25:195–203
    [Google Scholar]
  2. Azuma Y., Hosoyama A., Matsutani M., Furuya N., Horikawa H., Harada T., Hirakawa H., Kuhara S., Matsushita K. other authors 2009; Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res 37:5768–5783
    [Google Scholar]
  3. Chain P. S., Grafham D. V., Fulton R. S., Fitzgerald M. G., Hostetler J., Muzny D., Ali J., Birren B., Bruce D. C. other authors 2009; Genomics. Genome project standards in a new era of sequencing. Science 326:236–267
    [Google Scholar]
  4. Ciccarelli F. D., Doerks T., von Mering C., Creevy C. J., Snel B., Bork P. 2006; Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287
    [Google Scholar]
  5. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A. other authors 1995; Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512
    [Google Scholar]
  6. Flicek P., Birney E. 2009; Sense from sequence reads: methods for alignment and assembly. Nat Methods 6 (Suppl. 11):S6–S12
    [Google Scholar]
  7. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Bult C. J., Kerlavage A. R., Sutton G. other authors 1995; The minimal gene complement of Mycoplasma genitalium. Science 270:397–403
    [Google Scholar]
  8. Gil R., Silva F. J., Zientz E., Delmotte F., González-Candelas F., Latorre A., Rausell C., Kamerbeek J., Gadau J. other authors 2003; The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci U S A 100:9388–9393
    [Google Scholar]
  9. Gil R., Silva F. J., Peretó J., Moya A. 2004; Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68:518–537
    [Google Scholar]
  10. Han C., Sikorski J., Lapidus A., Nolan M., Del Rio T. G., Tice H., Cheng J.-F., Lucas S., Chen F. other authors 2009; Complete genome sequence of Kangiella koreensis type strain (SW-125T). Stand Genomic Sci 1: 3
    [Google Scholar]
  11. Klasson L., Andersson S. G. 2004; Evolution of minimal-gene-sets in host-dependent bacteria. Trends Microbiol 12:37–43
    [Google Scholar]
  12. Kyrpides N. C. 2009; Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol 27:627–632
    [Google Scholar]
  13. López-Sánchez M. J., Neef A., Peretó J., Patiño-Navarrete R., Pignatelli M., Latorre A., Moya A. 2009; Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PLoS Genet 5:e1000721
    [Google Scholar]
  14. Ma Y. F., Zhang Y., Zhang J. Y., Chen D. W., Zhu Y., Zheng H., Wang S. Y., Jiang C. Y., Zhao G. P., Liu S. J. 2009; The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments. Appl Environ Microbiol 75:6812–6819
    [Google Scholar]
  15. McCutcheon J. P., McDonald B. R., Moran N. A. 2009; Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci U S A 106:15394–15399
    [Google Scholar]
  16. Moran N. A., Baumann P. 2000; Bacterial endosymbionts in animals. Curr Opin Microbiol 3:270–275
    [Google Scholar]
  17. Moya A., Gil R., Latorre A. 2009; The evolutionary history of symbiotic associations among bacteria and their animal hosts: a model. Clin Microbiol Infect 15 :Suppl. 111–13
    [Google Scholar]
  18. Mushegian A. R., Koonin E. V. 1996; A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93:10268–10273
    [Google Scholar]
  19. Nakabachi A., Yamashita A., Toh H., Ishikawa H., Dunbar H. E., Moran N. A., Hattori M. 2006; The160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267
    [Google Scholar]
  20. Nolan M., Tindall B. J., Pomrenke H., Lapidus A., Copeland A., Del Rio T. G., Lucas S., Chen F., Tice H. other authors 2009; Complete genome sequence of Rhodothermus marinus type strain (R-10T . Stand Genomic Sci 1: 3
    [Google Scholar]
  21. Pukall R., Lapidus A., Nolan M., Copeland A., Del Rio T. G., Lucas S., Chen F., Tice H., Cheng J.-F. other authors 2009; Complete genome sequence of Slackia heliotrinireducens type strain (RSH 1T . Stand Genomic Sci 1: 3
    [Google Scholar]
  22. Reeves G. A., Talavera D., Thornton J. M. 2009; Genome and proteome annotation: organization, interpretation and integration. J R Soc Interface 6:129–147
    [Google Scholar]
  23. Tamames J., Gil R., Latorre A., Peretó J., Silva F. J., Moya A. 2007; The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol Biol 7:181
    [Google Scholar]
  24. Tauch A., Schneider J., Szczepanowski R., Tilker A., Viehoever P., Gartemann K. H., Arnold W., Blom J., Brinkrolf K. other authors 2008; Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. J Biotechnol 136:22–30
    [Google Scholar]
  25. Tettelin H., Masignani V., Cieslewicz M. J., Donati C., Medini D., Ward N. L., Angiuoli S. V., Crabtree J., Jones A. L. other authors 2005; Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 102:13950–13955
    [Google Scholar]
  26. Ussery D. W., Hallin P. F. 2004a; Genome update: length distributions of sequenced prokaryotic genomes. Microbiology 150:513–516
    [Google Scholar]
  27. Ussery D. W., Hallin P. F. 2004b; Genome update: AT content in sequenced prokaryotic genomes. Microbiology 150:749–752
    [Google Scholar]
  28. Ussery D. W., Wassenaar T. M., Borini S. 2009 Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists London, UK: Springer;
  29. Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N. N., Kunin V., Goodwin L., Wu M. other authors 2009; A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056–1060
    [Google Scholar]
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