Submitted to: Molecular Genetics and Genomics
Publication Type: Book / Chapter
Publication Acceptance Date: 9/9/2004
Publication Date: 3/18/2005
Citation: Chen, J. 2005. Genomic exploration of produce degradation. Molecular Genetics and Genomics. In: Lamikanra, O., Imam, S., Ukuku, D., editors. Produce Degradation Pathways and Prevention. Boca Raton, Fl: CRC Press. p. 1-18.
Interpretive Summary: The whole genome sequences of many plant pathogenic bacteria including the soft-rot erwiniae are becoming available in public database. One important issue in genomics is to extract important information of genome sequences. By comparing a large number of the DNA sequences from field strains with the complete genome sequence of model strains, more genetic information about the bacterial population and host-pathogen interactions can be unveiled. While new analytical tools such as microarray are important for genomic study, many of the already available technology can also make significant contributions. For example, strain specific DNA fragments have historically been used for identification purpose without knowing their genetic functions. In the genomic era, these fragments can be sequenced and their genetic nature can be elucidated utilizing genome sequence databases within a short period of time. Such efforts will have profound impact on the population genomic of soft-rot erwiniae. .
Technical Abstract: The use of molecular biology has led to significant advances in the research of soft rot erwiniae. By comparing the arrangement of DNA along entire genomes, more genetic information about the bacteria and host-pathogen interactions can be unveiled. This provides a base for further function analysis. While new analytical tools such as microarray are important for genomic study, many of the already available technology can also make significant contributions. This is particularly the case for random sampling tools that are used to test a large number of bacterial strains. For example, strain specific DNA fragment can be identified from random sampling analysis. The genetic nature of the specific DNA is then elucidated through sequences analysis utilizing genome sequence databased. In such a case, whole genome sequences from model strains serve as the system core to screen for new genetic information from strains of different sources. The whole genome sequences from model strain and the partial sequences from field strains together form a more complete database representing the soft-rot erwiniae population genome, and further facilitate research related to the pathogen.