Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main X. fastidiosa subspecies, which have allopatric origins: fastidiosa, multiplex and pauca The origin of recombinogenic subspecies morus and sandyi also was assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of a pauca subclade (7.62x10-7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. Relative effect of recombination compared to point mutation was calculated (r/m = 2.259). Evidence of recombination was uncovered in the core genome alignment; subsp. fastidiosa in the USA was less prone to recombination with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from subsp. fastidiosa Interestingly for subsp. morus, which was initially thought to be the outcome of genome-wide recombination between fastidiosa and multiplex, inter-subspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of citrus strains containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both fastidiosa and multiplex In summary, our data provide new insights in the evolution and epidemiology of this plant pathogen.ImportanceXylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled dataset for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades, to compare genome content at the subspecies level, and used a molecular dating approach to infer evolutionary rate of X. fastidiosa The results demonstrate that recombination is important in shaping genomes of X. fastidiosa, and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology. Copyright © 2019 American Society for Microbiology.
Journal: Applied and environmental microbiology