Genomic Exploration of Produce Degradation 3
attempt to demonstrate that many “old” DNA analysis tools are still useful or even
critical for soft rot erwina research in the genomic era.
1.1.1 GENOTYPE VS. PHENOTYPE
Characterization or identification of useful and unique features is the first step toward
the study of a microorganism. Classically, the bacterial phenome is used. The
phenotype of an organism can be described as the sum of its genotype and the effect
of the surrounding environment:
Phenotype = Genotype + Environment (1)However, the environmental factor is usually highly variable, particularly under
field conditions, resulting in inconsistent phenotypic variations, commonly regarded as
“atypical.” Shifting the environmental factor to the other side of the equation, genotypic
study of an organism becomes unaffected, or less affected, by the environment:
Genotype = Phenotype – Environment (2)Although formula (1) and formula (2) may oversimplify the genome–phenome
relationship, they illustrate the advantage of genomic analysis. In most cases, geno-
typic characterization is complementary to phenotypic characterization. In this dis-
cussion, genome refers to all organismal DNA. Genomic analysis can be done at
both global (whole genome sequence) and partial (DNA segment) levels. In either
case, the quality of analysis is directly related to the quality of the database used.
A genomic database can be in the form of either a nucleotide sequence or a coding
representation describing the status of DNA nucleotide variations.
DNA sequence databases are the most exchangeable among researchers. Genome
sequencing is used to identify the linear arrangement of all bases in an organism’s
DNA, commonly a combination of shotgun-sequencing and a gap-closure. Bioin-
formatics is used to analyze the sequence data to predict gene function, protein and
RNA structure, gene regulation, genome organization, and the phylogenetic history
of genes and gene families. Because of the large volume of data, specifically devel-
oped computer software is always required to assist the analysis. One popular
program for sequence comparison is BLAST (Altschul et al., 1997). There are many
other programs available on the Internet or from commercial sources, depending on the
goal of the analysis. Functional genomic approaches, such as gene disruption and
replacement experiments, are used to confirm the biological functions predicted from
sequence analysis. After all, the study of genomes, which includes DNA sequencing,
gene function, and genome structure and evolution, is referred to as genomics.
1.2 SEQUENCE GENOMICS
1.2.1 WHOLE GENOME SEQUENCING
Microbial genomics actually began in virology. The small genome size of viruses
makes it feasible to determine the whole nucleotide (DNA or RNA) sequence and