Tsai, C.-W. | Search bioRxiv

bioRxiv2021

Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of crops and industries. Xylella fastidiosa subspecies fastidiosa causes disease in grapevines (Pierces disease of grapevines, PD), a current problem in the United States (US), Spain, and Taiwan. We studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the US and two from Spain. Phylogenetic relationships, haplotype network, and genetic diversity analyses confirm that subsp. fastidiosa was recently introduced into Taiwan from the Southeast US (i.e., the PD-I lineage in Georgia based on available data). Recent core genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity, particularly in the Houli District of Taichung City in Central Taiwan. Unexpectedly, despite comprehensive sampling of all regions with high PD incidences in Taiwan, the genetic diversity observed include contributions through recombination from unknown donors, suggesting that higher diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis. In summary, this study improved our understanding of the genetic diversity of PD-causing subsp. fastidiosa after invasion to a new region.

genomics↗

bioRxiv2021

Complete genome sequence of Xylella taiwanensis and comparative analysis of virulence gene content with Xylella fastidiosa

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 were 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 PLS229T. 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. Contribution to the FieldXylella fastidiosa is a plant-pathogenic bacterium with multiple subspecies that are major threats to agriculture in America and Europe. Although extensive research has been conducted, comparative analysis of this species with other bacteria is lacking due to the unavailability of known close relatives. In this work, we report the complete genome sequence of Xylella taiwanensis, a newly described species within the same genus. This new data set and our focused analysis helped to better understand the evolutionary relationships among different Xylella lineages and their genomic diversity. Moreover, detailed examination of their virulence genes identified those that are either highly conserved or variable, providing promising candidates for future studies to further investigate the molecular mechanisms of Xylella virulence.

genomics↗