Draft Genome Sequence of Xylella fastidiosa Pear Leaf Scorch Strain in Taiwan

Emerging plant diseases frequently have significant economic, environmental, cultural, and social impacts. The prediction of new disease emergence, associated with new pathogens or not, remains a difficult and controversial topic. The main factors driving epidemics are often only identified several years after outbreaks, generally revealing that a limited number of factors are associated with the emergence of specific groups of pathogens. This pattern is illustrated in the insect-borne xylem-limited bacterium Xylella fastidiosa, an organism associated with several new plant diseases in different regions of the globe. Research during the last decade focusing on several severe disease outbreaks has led to substantial changes in our understanding of X. fastidiosa biology, ecology, and evolution. This new information has not only led to new insights into aspects of the biology of this bacterium and its interactions with plant and insect hosts, but also made available a phylogenetic framework that has allowed for better inferences concerning factors leading to the emergence of diseases. Here we identify and discuss these main pathways leading to epidemics caused by X. fastidiosa. Our ultimate goal was to raise critical questions and issues for academics and regulatory agencies alike, since the information generated during the last decade has both raised new questions but also clarified old ones.

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“…4). A distant relative is found in Taiwan (Su et al 2014), but should probably be classified as a separate species (see Fig. 3).…”

Section: Biology Of a Plant And Insect Colonizermentioning

confidence: 99%

How Do Plant Diseases Caused byXylella fastidiosaEmerge?

2015

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“…Other reports of introductions have been described, such as the identification of X. fastidiosa subsp. fastidiosa in Taiwan (11) and the presence of X. fastidiosa subsp. pauca in Central America (4).…”

mentioning

confidence: 96%

Genomic Diversity and Recombination among Xylella fastidiosa Subspecies

Vanhove

Retchless

Sicard

et al. 2019

Appl Environ Microbiol

114

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Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca. The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 ϫ 10 Ϫ7 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. The relative effect of recombination in comparison to point mutation was calculated (r/m ϭ 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States 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 X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa. Interestingly, for X. fastidiosa subsp. morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex. In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen. IMPORTANCE Xylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa. The results demonstrate that recombination is important in shaping the 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.

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“…A distant relative found in Taiwan on Nashi pears (Leu & Su, ) is another species named Xylella taiwanensis (Su et al ., ) . However, X. fastidiosa was also confirmed on grapevine in Taiwan (Su et al ., ). The presence of X. fastidiosa on almond and grapevine in Iran (Amanifar et al ., ) was reported (based on isolation and pathogenicity tests, but so far strain(s) are not available).…”

Section: Introductionmentioning

confidence: 97%

PM 7/24 (3) Xylella fastidiosa

2018

EPPO Bulletin

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Draft Genome Sequence of Xylella fastidiosa Pear Leaf Scorch Strain in Taiwan

Cited by 31 publications

References 19 publications

How Do Plant Diseases Caused byXylella fastidiosaEmerge?

How Do Plant Diseases Caused byXylella fastidiosaEmerge?

Genomic Diversity and Recombination among Xylella fastidiosa Subspecies

PM 7/24 (3) Xylella fastidiosa

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