Genetic diversity and population structure of Pseudomonas savastanoi , an endemic pathogen of the Mediterranean area, re
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ORIGINAL ARTICLE
Genetic diversity and population structure of Pseudomonas savastanoi, an endemic pathogen of the Mediterranean area, revealed up to strain level by the MLVA assay Yaseen Jundi Rahi 1,2 & Silvia Turco 1 & Maria Claudia Taratufolo 1 & Marta Tatì 1 & Matteo Cerboneschi 3 Stefania Tegli 3 & Franco Valentini 2 & Annamaria D’Onghia 2 & Nicola Sante Iacobellis 4 & Giorgio Mariano Balestra 1 & Angelo Mazzaglia 1
&
Received: 12 December 2019 / Accepted: 3 June 2020 # Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2020
Abstract Pseudomonas savastanoi is a bacterial species included in the Pseudomonas syringae complex. It is further sub-typed in pathovars which are the causal agents of a group of diseases of woody plants, such as the “knot disease” on olive and oleander and the bacterial canker on ash. Given its long-established presence in the Mediterranean area, the pathogen causing the aforementioned diseases can be considered endemic. Here, an MLVA approach was developed to assess the genetic relationships among and within those pathovars, with a specific focus on P. savastanoi pv. savastanoi. By analyzing the genome of the P. savastanoi pv. savastanoi strain NCPPB 3335 (accession n° CP008742), 14 Tandem Repeat (TR) loci were identified and the corresponding primers were designed and used for the amplification of genomic DNAs from 84 strains belonging to Pseudomonas savastanoi pathovars. Data were analyzed using different approaches, such as hierarchical clustering, STRUCTURE, and k-means clustering with DAPC to evaluate the effectiveness of the assay in describing pathovars and population structure of the pathogen. Results reveal a very complex articulation of genetic relationships, as expected from a long-time evolving pathogen, while providing the possibility to discriminate the pathovars between each other. At intra-pathovar level, the MLVA assay clusters isolates mainly according to their hosts and geographic origin. This resulted particularly useful in the identification and tracking of P. savastanoi populations at local level. Keywords Knot disease . VNTR . MLVA . DAPC . Population structure
Introduction The term “knot disease” in plant pathology describes the excessive growth of plant tissues or organs that leads to
* Angelo Mazzaglia [email protected] 1
Department of Agricultural and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
2
CIHEAM-Mediterranean Agronomic Institute of Bari, Via Ceglie 9, 70010 Valenzano, Ba, Italy
3
Agrifood Production and Environmental Sciences (DISPAA), University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy
4
School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell’Ateneo Lucano, 85100 Potenza, Italy
hyperplastic and/or hypertrophic masses in the shape of tumors or knots. These formations can be clearly observed on the aerial parts of diseased plants mostly on the woody parts of the plant such as stem, branches, or twigs and, more rarely, on le
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