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.

Fig 1.

Whole-genome comparison of three Xylella strains. A comparative analysis of the three Xf genomes was performed by using protein clustering algorithms. The numerals represent the number of clusters of related protein families.

Fig 2.

Visualization of orthologous chromosomal regions encoding the IncP conjugal transfer gene cluster centered around RXFA02052: 1-trbB; 2-trbC; 3-trbD; 4-trbE; 5-trbF; 6-trbG; 7-trbH; 8-trbI; 9-trbJ; 10-trbK; 11-trbL; 12-trbN. Dotted lines denote that the region is part of a putative mobile element (e.g., insertion element). The chromosomal copy of the XFA IncP cluster is shown here. The orthologous ORFs are represented by similar color shading.

Fig 3.

XFX and XFY strains are more closely similar to each other than to the XFA strain. Pair-wise comparisons based on (A) protein and (B) DNA sequence identity of the ORFs from each of the Xf protein clusters shared between all three strains.