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Applied and Environmental Microbiology, December 2005, p. 7716-7723, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.7716-7723.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

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

Q. Zhang,^1, U. Melcher,² L. Zhou,³ F. Z. Najar,³ B. A. Roe,³ and J. Fletcher^1*

Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma 74078,¹ Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078,² Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019³

Received 21 February 2005/ Accepted 28 July 2005

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.

Present address: Boyce Thompson Institute, Cornell University, Ithaca, NY 14853.

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