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The bacterial genus  Xylella  contains plant pathogens that are major threats to agriculture in America and Europe. Although extensive research was conducted to characterize different subspecies of  Xylella fastidiosa  ( Xf ), comparative analysis at above-species levels was lacking due to the unavailability of appropriate data sets. Recently, a bacterium that causes pear leaf scorch (PLS) in Taiwan was described as the second  Xylella  species (i.e.,  Xylella taiwanensis ;  Xt ). In this work, we report the complete genome sequence of  Xt  type strain PLS229 T . The genome-scale phylogeny provided strong support that  Xf  subspecies  pauca  ( Xfp ) is the basal lineage of this species and  Xylella  was derived from the paraphyletic genus  Xanthomonas . Quantification of genomic divergence indicated that different  Xf  subspecies share ∼87–95% of their chromosomal segments, while the two  Xylella  species share only ∼66–70%. Analysis of overall gene content suggested that  Xt  is most similar to  Xf  subspecies  sandyi  ( Xfs ). Based on the existing knowledge of  Xf  virulence genes, the homolog distribution among 28  Xylella  representatives was examined. Among the 11 functional categories, those involved in secretion and metabolism are the most conserved ones with no copy number variation. In contrast, several genes related to adhesins, hydrolytic enzymes, and toxin-antitoxin systems are highly variable in their copy numbers. Those virulence genes with high levels of conservation or variation may be promising candidates for future studies. In summary, the new genome sequence and analysis reported in this work contributed to the study of several important pathogens in the family Xanthomonadaceae.

Complete Genome Sequence of Xylella taiwanensis and Comparative Analysis of Virulence Gene Content With Xylella fastidiosa