Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot on commercial, ornamental and forest Prunus species. Outbreaks can result in severe economic losses to fruit quality and yield, branch/tree dieback, and orchard devastation, particularly on peach, apricot, nectarine and plum. This stone is endemic in the USA, NZ and is a quarantine regulated pathogen in Europe and elsewhere, compounding economic loss with eradication and regulatory expenses. Wide host range and climate change patterns portend potential increased invasion risk of this pathogen. Despite the regulatory and economic significance of Xap, almost nothing is known about the genetics of Xap compared to other xanthomonads. To fill this gap, a genome sequencing and comparative genomics approach were undertaken. We have sequenced the complete genome of a genotypic-representative Xap strain from Europe (Italy, CFBP 5530). This is the first complete genome sequence for this species. Paired-end 454-pyrosequencing and primer walking on a fosmid library gave 3 contigs. The chromosome is 4.85 Mb with 65.6% GC ratio and 3,912 predicted CDS. Xap has a unique 41.2 kb plasmid with a 62.3% GC ratio and 45 CDS. Comparative genomics with other Xanthomonads was used to identify X. arboricola-specific genes indicating features relevant to differential host specificity and virulence mechanisms. Among those, composition and role of type III secretion system effectors repertoires was surveyed within all six X. arboricola pathovars. Applied genomics has identified over 90 VNTR, several of which are currently being used to examine biodiversity and epidemiology of Xap and related pathovars, and design of improved diagnostics. This first complete genome sequence was also successfully used as a template to perform genomic assembly via mapping of short reads of several isolates from related pathovars. For example, the genome of a Xap isolate GBBC 2038 from the ornamental P. laurocerasus was assembled into 97 contigs. These two genomes present very high identity, the main difference being the presence of 10 kb genomic island in the ornamental isolate. Applied and comparative genomics improved our knowledge on host specificity and biodiversity of Xap, and allowed the development of efficient methods for detection of this plant disease. Overall, the availability of the first genome of X. arboricola constitutes a precious knowledge base for better comprehension of all other X. arboricola pathovars.
|Title of host publication||First International Congress for Bacterial Diseases of Stone Fruits and Nuts. Joint meeting of European COST 873 and ISHS, EHT Zürich|
|Publication status||Published - 15-Feb-2012|
|Event||First International Congress for Bacterial Diseases of Stone Fruits and Nuts - Zürich, Switzerland|
Duration: 14-Feb-2012 → 17-Feb-2012