Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence.

Molecular Plant Pathology
Boris A Vinatzer, Shuangchun Yan

Abstract

Hundreds of bacterial genomes including the genomes of dozens of plant pathogenic bacteria have been sequenced. These genomes represent an invaluable resource for molecular plant pathologists. In this review, we describe different approaches that can be used for mining bacterial genome sequences and examples of how some of these approaches have been used to analyse plant pathogen genomes so far. We review how genomes can be mined one by one and how comparative genomics of closely related genomes releases the true power of genomics. Databases and tools useful for genome mining that are publicly accessible on the Internet are also described. Finally, the need for new databases and tools to efficiently mine today's plant pathogen genomes and hundreds more in the near future is discussed.

References

Oct 20, 1995·Science·V E VelculescuK W Kinzler
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 28, 1998·Nucleic Acids Research·S L SalzbergO White
Jan 27, 1999·Bioinformatics·S R Eddy
Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Jan 11, 2000·Nucleic Acids Research·J D PetersonO White
Aug 3, 2001·Genome Research·UNKNOWN Gene Ontology Consortium
Dec 26, 2001·Bioinformatics·B E SuzekS L Salzberg
Feb 2, 2002·Nature·M SalanoubatC A Boucher
Feb 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Derrick E FoutsAlan Collmer
May 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Tanja Petnicki-OcwiejaJames R Alfano
Dec 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·Makoto OhnishiTetsuya Hayashi
Feb 14, 2003·Bioinformatics·William HsiaoFiona S L Brinkman
Jul 9, 2003·Briefings in Bioinformatics·Matt Berriman, Kim Rutherford
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Sep 13, 2003·BMC Bioinformatics·Roman L TatusovDarren A Natale
Nov 18, 2003·Proceedings of the National Academy of Sciences of the United States of America·Michael A JacobsColin Manoil
Dec 4, 2003·Journal of Biotechnology·Daniela BüttnerUlla Bonas
Dec 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Hideo MatsumuraRyohei Terauchi
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Feb 7, 2004·Cellular Microbiology·Jean T Greenberg, Nan Yao
Apr 22, 2004·Nature Reviews. Microbiology·Ulrich DobrindtJörg Hacker
Jul 3, 2004·Genome Research·Aaron C E DarlingNicole T Perna
Jul 17, 2004·Bioinformatics·Peter F Hallin, David W Ussery
Jul 21, 2004·Proceedings of the National Academy of Sciences of the United States of America·K S BellI K Toth
Jul 31, 2004·Annual Review of Phytopathology·James R Alfano, Alan Collmer
May 13, 2005·Plant Physiology·Chatchawan JantasuriyaratGuo-Liang Wang
Jun 25, 2005·Bioinformatics·Tim J CarverJulian Parkhill
Jul 7, 2005·Genome Research·Eric J AlmAdam P Arkin
Jul 8, 2005·Microbiology·Dawn FieldGareth A Wilson
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Aug 4, 2005·Bioinformatics·J C AbbottB G Spratt
Dec 31, 2005·Nucleic Acids Research·Robert D FinnAlex Bateman
Dec 31, 2005·Nucleic Acids Research·Victor M MarkowitzNikos C Kyrpides
Dec 31, 2005·Nucleic Acids Research·Natalia MaltsevMark D'Souza

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