Produce Degradation Pathways and Prevention

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0-8493-1902-1/05/$0.00+$1.
© 2005 by CRC Press

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Genomic Exploration

of Produce Degradation

J. Chen

USDA, ARS, PWA, San Joaquin Valley Agricultural Sciences

Center, 9611 South Riverbend Ave., Parlier, CA

CONTENTS

1.1 Introduction ...................................................................................................... 1
1.1.1 Genotype vs. Phenotype ...................................................................... 3
1.2 Sequence Genomics ......................................................................................... 3
1.2.1 Whole Genome Sequencing................................................................. 3
1.2.2 Sample Sequencing .............................................................................. 5
1.2.3 Sequences from rrn Operons ............................................................... 6
1.2.4 Other Genes.......................................................................................... 7
1.3 DNA Genomics ................................................................................................ 9
1.3.1 DNA-DNA Homology ......................................................................... 9
1.3.2 Random Genome Sampling ................................................................. 9
1.3.3 Genomic Subtraction.......................................................................... 11
1.4 Summary ........................................................................................................ 14
References................................................................................................................ 14

1.1 INTRODUCTION

An important aspect of learning to control microbial degradation of produce requires
understanding the degradation microorganisms. Recent advancements in bacterial
genome sequencing have created unprecedented amounts of genetic information.
Analysis of genome data offers a new perspective on microbial research and has
enhanced our understanding of produce degradation. In the genomic era, additional
genes with broader functions are expected to be discovered at a faster pace. Genome
study affects not only on the study of genes, but also other areas such bacterial
evolution, ecology, and systematics. From a population point of view, genomics
expands our understanding of model bacterial strains and helps in the exploration
of bacterial strains in all ecological niches. Soft rot erwinia are a group of bacterial
pathogens that cause both pre- and postharvest rot in a broad range of fresh produce.
The molecular biology research on soft rot erwinia in the past two decades has led
to significant discoveries of genes and mechanisms of pathogenicity (Collmer and
Keen,1986; Kotoujansky, 1987; Hugouvieux-Cotte-Pattat et al., 1996; Toth et al.,