AUTHOR=Weng Ling-Wei , Lin Yu-Chen , Su Chiou-Chu , Huang Ching-Ting , Cho Shu-Ting , Chen Ai-Ping , Chou Shu-Jen , Tsai Chi-Wei , Kuo Chih-Horng 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.684092

DOI=10.3389/fmicb.2021.684092

ISSN=1664-302X

ABSTRACT=<p>The bacterial genus <italic>Xylella</italic> contains plant pathogens that are major threats to agriculture in America and Europe. Although extensive research was conducted to characterize different subspecies of <italic>Xylella fastidiosa</italic> (<italic>Xf</italic>), 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 <italic>Xylella</italic> species (i.e., <italic>Xylella taiwanensis</italic>; <italic>Xt</italic>). In this work, we report the complete genome sequence of <italic>Xt</italic> type strain PLS229<sup>T</sup>. The genome-scale phylogeny provided strong support that <italic>Xf</italic> subspecies <italic>pauca</italic> (<italic>Xfp</italic>) is the basal lineage of this species and <italic>Xylella</italic> was derived from the paraphyletic genus <italic>Xanthomonas</italic>. Quantification of genomic divergence indicated that different <italic>Xf</italic> subspecies share ∼87–95% of their chromosomal segments, while the two <italic>Xylella</italic> species share only ∼66–70%. Analysis of overall gene content suggested that <italic>Xt</italic> is most similar to <italic>Xf</italic> subspecies <italic>sandyi</italic> (<italic>Xfs</italic>). Based on the existing knowledge of <italic>Xf</italic> virulence genes, the homolog distribution among 28 <italic>Xylella</italic> 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.</p>