Abstract
High rates of homologous recombination (HR) in the bacterial plant pathogen Xylella fastidiosa have been previously detected. This study aimed to determine the extent and explore the ecological significance of HR in the genomes of recombinants experimentally generated by natural transformation and wild-type isolates. Both sets of strains displayed widespread HR and similar average size of recombined fragments consisting of random events (2–10 kb) of inter- and intrasubspecific recombination. A significantly higher proportion and greater lengths (>10 kb, maximum 31.5 kb) of recombined fragments were observed in subsp. morus and in strains isolated in Europe from intercepted coffee plants shipped from the Americas. Such highly recombinant strains pose a serious risk of emergence of novel variants, as genetically distinct and formerly geographically isolated genotypes are brought in close proximity by global trade. Recently recombined regions in wild-type strains included genes involved in regulation and signaling, host colonization, nutrient acquisition, and host evasion, all fundamental traits for X. fastidiosa ecology. Identification of four recombinant loci shared between wild-type and experimentally generated recombinants suggests potential hotspots of recombination in this naturally competent pathogen. These findings provide insights into evolutionary forces possibly affecting the adaptive potential to colonize the host environments of X. fastidiosa.
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Acknowledgements
This project was funded by Agriculture and Food Research Initiative competitive grant no. 2015-67014-23085 from the USDA National Institute of Food and Agriculture, and HATCH AAES (Alabama Agricultural Experiment Station) program provided to N.P and L.D, and partly supported by research grant OS 2015330 of the Ministry of Economic Affairs in the Netherlands. We thank the Alabama Supercomputing Authority for granting access to their high-performance computing platform.
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Potnis, N., Kandel, P.P., Merfa, M.V. et al. Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa. ISME J 13, 2319–2333 (2019). https://doi.org/10.1038/s41396-019-0423-y
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DOI: https://doi.org/10.1038/s41396-019-0423-y
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