Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

Abstract

Xylella fastidiosa (Xf ) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two ''gapped'' Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an ''in silico'' cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.

Prophage Genomics

“…Comparative prophage analysis in bacterial species that were sequenced in multiple strains (Streptococcus, Staphylococcus, and Salmonella strains) or in sister species (Listeria, Xanthomonas, and Xylella) all provided arguments against the maintenance of a given prophage profile over longer evolutionary times. Furthermore, microarray analysis and PCR scanning demonstrated that prophages were generally strain specific within a given bacterial species (7,13,15,39,63,150,161,169). In fact, there are examples from both pathogenic and commensal bacterial species where prophages represented the majority of the strainspecific DNA.…”

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

“…Published annotations indicate that these genomes each contain from 2,066 to 2,294 protein-coding sequences, 2 ribosomal RNA operons, 49-50 tRNA genes (43 different anti-codons), and 1 tmRNA gene (van Sluys et al 2003). Draft quality genomes are available for three other isolates, each appearing to be very similar to one of the finished genomes at the coarse scale (Bhattacharyya et al 2002;Schreiber et al 2010;Zhang et al 2011), as are contigs from the shotgun sequencing of a mixed sample of subspecies multiplex and sandyi (Bhattacharyya et al 2002;Nunney et al 2012). The diversity of available sequences will increase rapidly in the near future, as several projects are underway that are sequencing tens of genomes from isolates collected around the world.…”

Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

“…Recent genome comparisons involving Xf strains obtained from citrus, almond, and oleander plants broadened this scenario, suggesting that a series of conjugation-related ORFs found in Xf strains could have been acquired from soil-inhabiting bacteria (Bhattacharyya et al 2002a). Moreover, a large (∼67-kb) element present in the genome of Xf strain 9a5c was identified as a new prophage, probably derived from the Siphophage group of doublestranded bacteriophages (Bhattacharyya et al 2002b).…”