4 Produce Degradation: Reaction Pathways and their Prevention
allows genomic comparisons that otherwise would be difficult or even impossible
to perform with the early biotechnology. Viral genomics revolutionized plant virol-
ogy and resulted in novel strategies for virus research and disease control. The first
plant pathogenic bacterial genome sequence was completed with Xylella fastidiosa,
a pathogen causing citrus variegated chlorosis in Brazil (Simpson et al., 2000).
Because of the nutritional fastidiousness, X. fastidiosa was much less characterized
by classical biochemical and genetic approaches than many other bacterial plant
pathogens. The sequence data, however, immediately make possible the exploration
of the pathogenicity, biology, epidemiology, and evolution of the organism. Since
then, several other plant pathogen and plant symbiont genome sequences have been
published. More genome sequencing of plant pathogens, including pathogenic fungi,
has also been initiated; some of this research is in an advanced stage. The following
Web sites provide some of the most up-to-date genome sequencing information:
http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html
http://www.ncbi.nlm.nih.gov/genomes/MICROBES/InProgress.html
http://www.ncbi.nlm.nih.gov/genomes/FUNGI/funtab.htmlGenome sequencing projects have been initiated for two species of soft rot
erwinia. The Sanger Institute was funded by the Scottish Office (SEERAD) to
sequence the genome of E. carotovora subsp. atroseptica strain SCRI1043 (ATCC
BAA-672). The sequencing is now completed (http://www.sanger.ac.uk/Projects/E_
carotovora/). (Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva
MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K, Atkin R, Bason N, Brooks
K, Chillingworth T, Clark K, Doggett J, Fraser A, Hance Z, Hauser H, Jagels K,
Moule S, Norbertczak H, Ormond D, Price C, Quail MA, Sanders M, Walker D,
Whitehead S, Salmond GP, Birch PR, Parkhill J, and Toth IK. 2004. Genome
sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atrosep-
tica and characterization of virulence factors. Proc Natl Acad Sci U S A 27:11105-
10.) The genome is 5.064 Mb in length with a G+C content of 50.97%. TIGR and
University of Wisconsin, funded by USDA, are collaborating in sequencing Erwinia
chrysanthemi strain 3937 (http://www.ahabs.wisc.edu and http://www.tigr.org/tdb/
mdb/mdbinprogress.html). The sequencing is anticipated to be complete in 2004.
The unfinished sequence has total bases of 4,936,076 bp in 40 contigs (http://www.
ncbi.nlm.nih.gov/genomes/ framik.cgi?db=genome&gi=5110).
An elaborate genome sequence comparison both globally and locally (compar-
ative genomics) provides a valuable alternative to discover new genetic and phylo-
genetic information. The basic assumption is that many common features are shared
between different bacteria. Such conserved features may even cross the border
between plant and animal bacteria. For soft rot erwinia, it is assumed, and evidence
indicates, that they share an enterobacterial chromosomal “backbone” derived from
a common ancestor. Differences are attributed to extensive horizontal gene transfer,
genome rearrangements, gene duplication, sequence insertion/deletion, and nucle-
otide mutation into nonfunctional pseudogenes. Bacterial “lifestyle” changes and
varies from one to another in different ecological niches.