Abstract
BackgroundXanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content.ResultsThe Xf draft genome (4.2 Mb) was considerably smaller than most known Xanthomonas genomes (~5 Mb). Only half of the genes coding for TonB-dependent transporters and cell-wall degrading enzymes that are typically present in other Xanthomonas genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii) xcs, one of two Type II Secretion System coding regions in Xanthomonas, and iv) the genes coding for the glyoxylate shunt pathway. Conversely, the Xf genome revealed a high content of externally derived DNA and several uncommon, possibly virulence-related features: a Type VI Secretion System, a second Type IV Secretion System and a distinct Type III Secretion System effector repertoire comprised of multiple rare effectors and several putative new ones.ConclusionsThe draft genome sequence of LMG 25863 confirms the distinct phylogenetic position of Xf within the genus Xanthomonas and reveals a patchwork of both lost and newly acquired genomic features. These features may help explain the specific, mostly endophytic association of Xf with the strawberry plant.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-829) contains supplementary material, which is available to authorized users.
Highlights
Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU
A first de novo assembly using a single Paired-End (PE) Illumina short-read dataset (Table 1) did not meet our expectations: the contig number and N50-values of this initial draft genome sequence were on par with comparable assemblies of other Xanthomonas genomes (e.g. [24]), it was considerably smaller than anticipated (3,9 Mb instead of 5 Mb) and revealed an exceptionally high Insertion Sequences (IS) related repetitive DNA content
A second, Mate-Paired (MP) Illumina short-read dataset with a larger insert size was generated to avoid incomplete genome assembly caused by read ambiguity
Summary
Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. Xanthomonas fragariae (Xf ) is a bacterial strawberry pathogen and the cause of angular leaf spot. It was first described in the United States in 1962 [1] and has since spread globally. Under favourable conditions the pathogen may cause significant damage to both plant stock and strawberry production [2].
Published Version (Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have