HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Bell, K. S. Articles by Birch, P. R. J. Search for Related Content PubMed PubMed Citation Articles by Bell, K. S. Articles by Birch, P. R. J. Agricola Articles by Bell, K. S. Articles by Birch, P. R. J.

Sample sequencing of a selected region of the genome of Erwinia carotovora subsp. atroseptica reveals candidate phytopathogenicity genes and allows comparison with Escherichia coli

Unit of Mycology, Bacteriology and Nematology¹ and Unit of Genomics², Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK

Author for correspondence: Paul R. J. Birch. Tel: +44 1382 562731. Fax: +44 1382 562426. e-mail: pbirch{at}scri.sari.ac.uk

Genome sequencing is making a profound impact on microbiology. Currently, however, only one plant pathogen genome sequence is publicly available and no genome-sequencing project has been initiated for any species of the genus Erwinia, which includes several important plant pathogens. This paper describes a targeted sample sequencing approach to study the genome of Erwinia carotovora subsp. atroseptica (Eca), a major soft-rot pathogen of potato. A large insert DNA (approx. 115 kb) library of Eca was constructed using a bacterial artificial chromosome (BAC) vector. Hybridization and end-sequence data revealed two overlapping BAC clones that span an entire hrp gene cluster. Random subcloning and one-fold sequence coverage (>200 kb) across these BACs identified 25 (89%) of 28 hrp genes predicted from the orthologous hrp cluster of Erwinia amylovora. Regions flanking the hrp cluster contained orthologues of known or putative pathogenicity operons from other Erwinia species, including dspEF (E. amylovora), hecAB and pecSM (E. chrysanthemi), sequences similar to genes from the plant pathogen Xylella fastidiosa, including haemagglutinin-like genes, and sequences similar to genes involved in rhizobacterium–plant interactions. Approximately 10% of the sequences showed strongest nucleotide similarities to genes in the closely related model bacterium and animal pathogen Escherichia coli. However, the positions of some of these genes were different in the two genomes. Approximately 30% of sequences showed no significant similarity to any database entries. A physical map was made across the genomic region spanning the hrp cluster by hybridization to the BAC library and to digested BAC clones, and by PCR between sequence contigs. A multiple genome coverage BAC library and one-fold sample sequencing are an effective combination for extracting useful information from important regions of the Eca genome, providing a wealth of candidate novel pathogenicity genes for functional analyses. Other genomic regions could be similarly targeted.

Keywords: draft sequencing, plant pathogen, bacterial genomics, enterobacterium

Abbreviations: BAC, bacterial artificial chromomsome; Eca, Erwinia carotovora subsp. atroseptica; Ecc, Erwinia carotovora subsp. carotovora

The GenBank accession numbers for the 424 sequences determined in this work are BH614193 to BH614616.

This article has been cited by other articles:

				V. Chow, G. Nong, and J. F. Preston Structure, Function, and Regulation of the Aldouronate Utilization Gene Cluster from Paenibacillus sp. Strain JDR-2 J. Bacteriol., December 15, 2007; 189(24): 8863 - 8870. [Abstract] [Full Text] [PDF]

				A. O. Avrova, S. C. Whisson, L. Pritchard, E. Venter, S. De Luca, I. Hein, and P. R. J. Birch A novel non-protein-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans Microbiology, March 1, 2007; 153(3): 747 - 759. [Abstract] [Full Text] [PDF]

				K. S. Bell, M. Sebaihia, L. Pritchard, M. T. G. Holden, L. J. Hyman, M. C. Holeva, N. R. Thomson, S. D. Bentley, L. J. C. Churcher, K. Mungall, et al. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors PNAS, July 27, 2004; 101(30): 11105 - 11110. [Abstract] [Full Text] [PDF]

				C. M. Rojas, J. H. Ham, W.-L. Deng, J. J. Doyle, and A. Collmer HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings PNAS, October 1, 2002; 99(20): 13142 - 13147. [Abstract] [Full Text] [PDF]