Draft genome sequencing of Xanthomonas fragariae reveals reduced genome size and distinct virulence related gene content

Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is known for its rather weak pathogenicity, fastidious growth on artificial media, its narrow host range and its taxonomically distinct but homogenous position within the otherwise complex genus Xanthomonas. As part of a broader pathogenicity study of Xf, the genome of a recent Belgian isolate (LMG 25863) was sequenced and assembled to draft status, with 105 contigs of more than 200 bp long. Remarkably, the Xf draft genome (4.2 Mb) was considerably smaller than most other Xanthomonas genomes (~5 Mb). Compared to other plant pathogenic Xanthomonas, Xf appeared to miss several genes/regions with a possible relevance to pathogenicity: i) an operon involved in the breakdown of phenolic compounds, ii) one of the two Type II Secretion System coding regions in Xanthomonas, iii) isocitrate lyase and malate synthase, responsible for the glyoxylate shunt pathway, and iv) two genes of the rfp gene cluster, rpfD and rpfI. Also, only half of the cellulolytic, hemicellulolytic and pectinolytic enzyme coding genes typically present in other Xanthomonas genomes were found in Xf. On the other hand, we identified possible virulence-related gene regions in Xf that are not common in other Xanthomonas genomes, with a Type VI Secretion System coding region being the most obvious one. Also, the Type III Secretion System effector repertoire in the Xf genome included several rare variable effectors such as xopC, xopE4, xopAF and xopAS, and some putatively new effectors. The Xf draft genome further revealed a high content of externally derived DNA: i) multiple copies of several Insertion Sequence (IS) elements, comparable to Xanthomonas oryzae, ii) a phage coding region, iii) 18-19 kb of sequence fragments with high similarity to Plasmid III (27 kb) of X. albilineans GPE GP73, and iv) a CRISPR associated gene cluster of the Yersinia pestis subtype with 40 related spacer sequences. The draft genome sequence of LMG 25863 affirms the distinct position of Xf within the genus Xanthomonas and reveals a patchwork of both lost and newly acquired pathogenicity related functions. It’s pathogenicity related distinguishing features may help explain the specific, mostly endophytic association of Xf with the strawberry plant system.