Vol. 57 No. 1 (2018)
Research Papers

Insights on a founder effect: the case of <em>Xylella fastidiosa</em> in the Salento area of Apulia, Italy

Matteo RAMAZZOTTI
University of Florence
Fabio CIMAGLIA
Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Lecce, Italy Dipartimento di Scienze delle Produzioni Agroalimentari e dell’Ambiente, Sezione di Patologia Vegetale ed Entomologia, Università degli Studi, Piazzale delle Cascine 28, 50144 Firenze, Italy
Antonia GALLO
Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Lecce, Italy
Francesco RANALDI
Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università degli Studi di Firenze, viale G.B. Morgagni 50, 50134, Firenze, Italy
Giuseppe SURICO
Dipartimento di Scienze delle Produzioni Agroalimentari e dell’Ambiente, Sezione di Patologia Vegetale ed Entomologia, Università degli Studi, Piazzale delle Cascine 28, 50144 Firenze, Italy
Giovanni MITA
Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Lecce, Italy
Gianluca BLEVE
Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Lecce, Italy
Guido MARCHI
Dipartimento di Scienze delle Produzioni Agroalimentari e dell’Ambiente, Sezione di Patologia Vegetale ed Entomologia, Università degli Studi, Piazzale delle Cascine 28, 50144 Firenze, Italy
Published February 14, 2018
Keywords
  • whole genomes,
  • phylogeny,
  • olive quick decline syndrome (OQDS)
How to Cite
[1]
M. RAMAZZOTTI, “Insights on a founder effect: the case of <em>Xylella fastidiosa</em&gt; in the Salento area of Apulia, Italy”, Phytopathol. Mediterr., vol. 57, no. 1, pp. 8-25, Feb. 2018.

Abstract

Xylella fastidiosa causing disease on different plant species has been reported in several European countries, since 2013. Based on multilocus sequence typing (MLST) results, there is evidence of repeated introductions of the pathogen in Spain and France. In contrast, in the Salento area of Apulia (Puglia) in Southern Italy, the existence of a unique Apulian MLST genotype of X. fastidiosa, causing the olive quick decline syndrome (OQDS; also referred to as “CoDiRO” or “ST53”) was proven, and this was tentatively ascribed to X. fastidiosa subsp. pauca. In order to acquire information on intra population diversity European Food Safety Authority (EFSA) has strongly called for the characterization of X. fastidiosa isolates from Apulia to produce the necessary data to better understand strain diversity and evolution. In this work, for the first time the existence of sub-variants within a set of  14 “ST53” isolates of X. fastidiosa collected from different locations was searched using DNA typing methods targeting the whole pathogen genome. Invariably, VNTR, RAPD and rep-PCR (ERIC and BOX motifs) analyses indicated that all tested isolates possessed the same genomic fingerprint, supporting the existence of predominant epidemiological strain in Apulia. To further explore the degree of clonality within this population, two isolates from two different Salento areas (Taviano and Ugento) were completely sequenced using PacBio SMRT technology. The whole genome map and sequence comparisons revealed that both isolates are nearly identical, showing less than 0.001% nucleotide diversity. However, the complete and circularized Salento-1 and Salento-2 genome sequences were different, in genome and plasmid size, from the reference strain 9a5c of X. fastidiosa subsp. pauca (from citrus), and showed a PCR-proved large genome inversion of about 1.7 Mb. Genome-wide indices ANIm and dDDH indicated that the three isolates of X. fastidiosa from Salento (Apulia, Italy), namely Salento-1, Salento-2, and De Donno, whose complete genome sequence has been recently released, share a very recent common ancestor. This highlights the importance of continuous and extensive monitoring of molecular variation of this invasive pathogen to understand evolution of adaptive traits, and the necessity for adoption of all possible measures to reduce the risk of new introductions that may augment pathogen diversity.

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