Intercepted isolates of Xylella fastidiosa in Europe reveal novel genetic diversity

Loconsole, Giuliana; Saponari, María; Boscia, D.; D’Attoma, Giusy; Morelli, Massimiliano; Martelli, G. P.; Almeida, Rodrigo P. P.

doi:10.1007/s10658-016-0894-x

Cited by 69 publications

(89 citation statements)

References 29 publications

(36 reference statements)

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“…Although not appropriate for the typing of closely related strains , MLST has been useful at the subspecies level of phylogenetic resolution (Almeida et al 2008;Yuan et al 2010). The portability of the system has allowed for fast identification of epidemic strains (Loconsole et al 2016), as well as host-pathogen associations among sympatric ST (Harris and Balci 2015). MLST was used to identify novel genetic diversity in South America, expanding the number of ST from 6 to 15.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, some recently published data emphasized that there is additional diversity within this species that has not been described, including within subsp. pauca (Loconsole et al 2016).…”

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confidence: 99%

“…pauca led to emergence of the citrus and coffee diseases mentioned above, which is possible yet not conclusively demonstrated based on available data (Nunney et al 2012). In addition to being the etiological agent of diseases in South America, X. fastidiosa subspecies pauca has now been reported from Costa Rica (Nunney et al 2014a) and Europe (Loconsole et al 2016;Saponari et al 2013). Despite the growing relevance due to its increasing geographical distribution, as well as crops to which it causes disease, the genetic diversity of subsp.…”

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confidence: 99%

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Homologous Recombination and Xylella fastidiosa Host–Pathogen Associations in South America

et al. 2017

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Homologous recombination affects the evolution of bacteria such as Xylella fastidiosa, a naturally competent plant pathogen that requires insect vectors for dispersal. This bacterial species is taxonomically divided into subspecies, with phylogenetic clusters within subspecies that are host specific. One subspecies, pauca, is primarily limited to South America, with the exception of recently reported strains in Europe and Costa Rica. Despite the economic importance of X. fastidiosa subsp. pauca in South America, little is known about its genetic diversity. Multilocus sequence typing (MLST) has previously identified six sequence types (ST) among plant samples collected in Brazil (both subsp. pauca and multiplex). Here, we report on a survey of X. fastidiosa genetic diversity (MLST based) performed in six regions in Brazil and two in Argentina, by sampling five different plant species. In addition to the six previously reported ST, seven new subsp. pauca and two new subsp. multiplex ST were identified. The presence of subsp. multiplex in South America is considered to be the consequence of a single introduction from its native range in North America more than 80 years ago. Different phylogenetic approaches clustered the South American ST into four groups, with strains infecting citrus (subsp. pauca); coffee and olive (subsp. pauca); coffee, hibiscus, and plum (subsp. pauca); and plum (subsp. multiplex). In areas where these different genetic clusters occurred sympatrically, we found evidence of homologous recombination in the form of bidirectional allelic exchange between subspp. pauca and multiplex. In fact, the only strain of subsp. pauca isolated from a plum host had an allele that originated from subsp. multiplex. These signatures of bidirectional homologous recombination between endemic and introduced ST indicate that gene flow occurs in short evolutionary time frames in X. fastidiosa, despite the ecological isolation (i.e., host plant species) of genotypes.

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Section: Discussionmentioning

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Homologous Recombination and Xylella fastidiosa Host–Pathogen Associations in South America

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“…Symptoms of OQDS include yellow and brown lesions on leaf tips and margins, extensive branch and twig dieback, and subsequent tree mortality (Saponari et al 2013). Multilocus sequence typing (MLST) and comparative genomic analyses of the draft genome of an oliveinfecting strain (Loconsole et al 2016) showed its genetic relatedness to X. fastidiosa subsp. pauca isolates.…”

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confidence: 99%

“…pauca in Central America. The discovery of the ST53, together with recent European Union interceptions of X. fastidiosa isolates harboring several new sequence types (Loconsole et al 2016), illustrates the limited knowledge on the diversity of this bacterium.…”

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Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America

et al. 2017

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Xylella fastidiosa is a plant-pathogenic bacterium recently introduced in Europe that is causing decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was recently clarified, showing it contains alleles that are monophyletic with those of subsp. pauca in South America. To more robustly determine the phylogenetic placement of ST53 within X. fastidiosa, we performed a comparative analysis based on single nucleotide polymorphisms (SNPs) and the study of the pan-genome of the 27 currently public available whole genome sequences of X. fastidiosa. The resulting maximum-parsimony and maximum likelihood trees constructed using the SNPs and the pan-genome analysis are consistent with previously described X. fastidiosa taxonomy, distinguishing the subsp. fastidiosa, multiplex, pauca, sandyi, and morus. Within the subsp. pauca, the Italian and three Costa Rican isolates, all belonging to ST53, formed a compact phylotype in a clade divergent from the South American pauca isolates, also distinct from the recently described coffee isolate CFBP8072 imported into Europe from Ecuador. These findings were also supported by the gene characterization of a conjugative plasmid shared by all the four ST53 isolates. Furthermore, isolates of the ST53 clade possess an exclusive locus encoding a putative ATP-binding protein belonging to the family of histidine kinase-like ATPase gene, which is not present in isolates from the subspecies multiplex, sandyi, and pauca, but was detected in ST21 isolates of the subspecies fastidiosa from Costa Rica. The clustering and distinctiveness of the ST53 isolates supports the hypothesis of their common origin, and the limited genetic diversity among these isolates suggests this is an emerging clade within subsp. pauca.

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Soil Biodiversity and Tree Crops Resilience

Ciancio

Gamboni²

2017

Soil Biological Communities and Ecosystem Resilience

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Intercepted isolates of Xylella fastidiosa in Europe reveal novel genetic diversity

Abstract: After the first confirmed outbreak of Xylella fastidiosa in the European

Cited by 69 publications

References 29 publications

Homologous Recombination and Xylella fastidiosa Host–Pathogen Associations in South America

Homologous Recombination and Xylella fastidiosa Host–Pathogen Associations in South America

Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America

Soil Biodiversity and Tree Crops Resilience

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