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Genomic Comparison of Plant Pathogenic and Nonpathogenic Serratia marcescens Strains by Suppressive Subtractive Hybridization

Zhang, Q., Melcher, U., Zhou, L., Najar, F. Z., Roe, B. A., Fletcher, J.
Applied and environmental microbiology 2005 v.71 no.12 pp. 7716-7723
Serratia marcescens, plant pathogenic bacteria, pathogenicity, strain differences, virulence, nucleic acid hybridization, nucleotide sequences, genes, genome, bacterial diseases of plants, Cucurbita pepo, zucchini, endophytes, Oryza sativa, rice, DNA primers, polymerase chain reaction
Cucurbit yellow vine disease (CYVD) is caused by disease-associated Serratia marcescens strains that have phenotypes significantly different from those of nonphytopathogenic strains. To identify the genetic differences responsible for pathogenicity-related phenotypes, we used a suppressive subtractive hybridization (SSH) strategy. S. marcescens strain Z01-A, isolated from CYVD-affected zucchini, was used as the tester, whereas rice endophytic S. marcescens strain R02-A (IRBG 502) was used as the driver. SSH revealed 48 sequences, ranging from 200 to 700 bp, that were present in Z01-A but absent in R02-A. Sequence analysis showed that a large proportion of these sequences resembled genes involved in synthesis of surface structures. By construction of a fosmid library, followed by colony hybridization, selection, and DNA sequencing, a phage gene cluster and a genome island containing a fimbrial-gene cluster were identified. Arrayed dot hybridization showed that the conservation of subtracted sequences among CYVD pathogenic and nonpathogenic S. marcescens strains varied. Thirty-four sequences were present only in pathogenic strains. Primers were designed based on one Z01-A-specific sequence, A79, and used in a multiplex PCR to discriminate between S. marcescens strains causing CYVD and those from other ecological niches.