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Background   Xanthomonas albilineans  causes leaf scald, a lethal disease of sugarcane.  X. albilineans  exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of  Xanthomonas . For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic  X. albilineans  strain GPE PC73 focused exclusively on distinctive genomic features shared with  Xylella fastidiosa —another xylem-limited  Xanthomonadaceae . The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of  X. albilineans , and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity.    Results  Comparative genomic analyses showed that most of the known pathogenicity factors from other  Xanthomonas  species are conserved in  X. albilineans , with the notable absence of two major determinants of the “artillery” of other plant pathogenic species of  Xanthomonas : the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific to  X. albilineans  that may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, no genes potentially involved in any offensive or counter-defensive mechanism specific to  X. albilineans  were identified, supposing that  X. albilineans  has a reduced artillery compared to other pathogenic  Xanthomonas  species. Particular attention has therefore been given to genomic features specific to  X. albilineans  making it more capable of evading sugarcane surveillance systems or resisting sugarcane defense systems.    Conclusions  This study confirms that  X. albilineans  is a highly distinctive species within the genus  Xanthomonas , and opens new perpectives towards a greater understanding of the pathogenicity of this destructive sugarcane pathogen.

Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels