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A Comprehensive Species to Strain Taxonomic Framework for Xanthomonas

September 2005 , Volume 95 , Number  9
Pages  1,098 - 1,111

J. L. W. Rademaker , F. J. Louws , M. H. Schultz , U. Rossbach , L. Vauterin , J. Swings , and F. J. de Bruijn

First, third, fourth, and seventh authors: MSU-DOE Plant Research Laboratory; seventh author: Department of Microbiology and NSF Center for Microbial Ecology, Michigan State University, East Lansing 48824; second author: Department Plant Pathology, North Carolina State University, Raleigh 27695; fifth and sixth authors: Laboratorium voor Microbiologie; sixth author: BCCM/LMG Bacteria Collection, Rijksuniversiteit Gent, Ledeganckstraat 35, B-9000 Ghent, Belgium; and fifth author: Applied Maths BVBA, Derbystraat 331, B-9051 Ghent, Belgium

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Accepted for publication 12 May 2005.

A comprehensive classification framework was developed that refines the current Xanthomonas classification scheme and provides a detailed assessment of Xanthomonas diversity at the species, subspecies, pathovar, and subpathovar levels. Polymerase chain reaction (PCR) using primers targeting the conserved repetitive sequences BOX, enterobacterial repetitive intergenic consensus (ERIC), and repetitive extragenic palindromic (REP) (rep-PCR) was used to generate genomic fingerprints of 339 Xanthomonas strains comprising 80 pathovars, 20 DNA homology groups, and a Stenotrophomonas maltophilia reference strain. Computer-assisted pattern analysis of the rep-PCR profiles permitted the clustering of strains into distinct groups, which correspond directly to the 20 DNA-DNA homology groups(genospecies) previously identified. Group 9 strains (X. axonopodis) were an exception and did not cluster together into a coherent group but comprised six subgroups. Over 160 strains not previously characterized by DNA-DNA hybridization analysis, or not previously classified, were assigned to specific genospecies based on the classification framework developed. The rep-PCR delineated subspecific groups within X. hortorum, X. arboricola, X. axonopodis, X. oryzae, X. campestris, and X. translucens. Numerous taxonomic issues with regard to the diversity, similarity, redundancy, or misnaming were resolved. This classification framework will enable the rapid identification and classification of new, novel, or unknown Xanthomonas strains that are pathogenic or are otherwise associated with plants.

Additional keywords: X. albilineans , X. bromi , X. cassavae , X. codiaei , X. cucurbitae , X. fragariae , X. hyacinthi , X. melonis , X. pisi , X. populi , X. sacchari , X. theicola , X. vasicola , X. vesicatoria .

© 2005 The American Phytopathological Society