2 Produce Degradation: Reaction Pathways and their Prevention
2003). In this chapter, advances in the population genomics of soft rot erwinia are
used to demonstrate the importance of genome analysis in the understanding and
control of produce degradation.
In the genus Erwinia, one noticeable development derived from genome analysis
is the bacterial taxonomy. Genome sequence analyses have unveiled new phylogenetic
relationships among Erwinia strains. Accordingly, reclassification of the bacterium has
been proposed at the genus, species, and subspecies levels (Kwon et al., 1997; Hauben
et al., 1998; Gardan et al., 2003). The soft rot erwinia have been regrouped into the
genus Pectobacterium, and several subspecies have been elevated to species (Hauben
et al., 1998; Gardan et al., 2003). Along this line, more accurate and sophisticated
identification tools have been developed or are emerging (Louws et al., 1999).
Both Erwinia and Pectobacterium are validly published names. In this discus-
sion, the name Erwinia will be used. The term soft rot erwinia is generically used
to refer to E. carotovora and E. chrysanthemi. The former is further divided into
subspecies including, E. carotovora subsp. atroseptica and E. carotovora subsp.
carotovora. Detailed discussions on the taxonomy and biology of soft rot erwinia
are available in a number of review publications (Starr and Chatterjee, 1972; Chat-
terjee and Starr, 1980; Barras et al., 1994; De Boer, 2003).
A bacterial taxon describes a population or a group of prokaryotic cells sharing
a level of similarity. A defined number of strains are sampled to represent the
population. Typically, one or more strains are selected as representatives for further
detailed characterization and even fewer are subjected to whole genome sequencing.
As such, the representative strain(s) does not contain all the genetic material in the
bacterial population. During the process of environmental adaptation, a bacterial
genome could be subject to base mutation, sequence insertion/deletion (indel),
horizontal gene transfer, and genome rearrangement (Pym and Brosch, 2000). Such
information is often related to bacterial pathogenicity and host specialization.
Genetic variations are usually acquired through genomic comparison involving more
strains from different sources.
Analyses of representative strains establish the main core of bacterial genomics,
but gaps in information remain. Filling in these gaps relies on frequent and even
extensive analyses of other bacterial strains in the population. In the past, this has
been the work of identifying new genetic elements, particularly those involved in
horizontal gene transfer, such as phages, plasmids, and transposons. Results from
recent genomic studies show that sequence insertion/deletion or indels and genomic
rearrangements are also important sources of genetic variation (Pym and Brosch,
2000; Britten et al., 2003).
The term genome analysis is defined as comparing and deducing information
from genomic DNA. For soft rot erwinia, the wave of whole-genome sequencing
has arrived. It can be certain that much new information has been generated and is
being published. Reviews regarding recent research advances in the genomics of
soft rot erwinia have been published (De Boer, 2003; Toth et al., 2003). Yet, it is
also true that much more new information is awaiting discovery. This chapter intends
to highlight some new developments in soft rot erwinia genomics and discuss bacterial
genomics from the population point of view. Efforts will be made to connect the results
of previous DNA-based population analyses to current genomic knowledge in an