Genetic variability of the stolbur phytoplasma vmp1 gene in grapevines, bindweeds and vegetables

Abstract

Aim: Evaluation of the genetic variability of stolbur phytoplasma infecting grapevines, bindweeds and vegetables, collected in different central and southern Italian regions. Materials and Results: Phytoplasma isolates belonging to stolbur subgroup 16SrXII‐A were subjected to molecular characterization by polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP), to investigate two different nonribosomal genes: tuf and vmp1. In grapevines, 32% of samples were infected by tuf‐a type and 68% by tuf‐b type, with different relative incidences in the regions surveyed. All herbaceous samples (bindweeds, tomato, tobacco, pepper, celery) were infected by tuf‐b. The gene vmp1 showed higher polymorphism in grapevines (nine profiles) than herbaceous plants (six) by RFLP analysis, in agreement with nucleotide sequences’ analysis and virtual digestions. Conclusions: The phylogenetic analysis of vmp1 gene sequences supports the RFLP data and demonstrates the accuracy of RFLP for preliminary assessments of genetic diversity of stolbur phytoplasmas and for screening different vmp types. Significance and Impact of the Study: Stolbur represents a serious phytosanitary problem in the areas under investigation, owing to heavy economic losses in infected grapevines and vegetables. Molecular information about the complex genotyping of the vmp1 gene provides useful data towards a better understanding of stolbur epidemiology. Moreover, this study clarifies some different vmp1 genotype classifications of stolbur, providing molecular data in comparison with previous investigations.

In-vineyard population structure of ‘Candidatus Phytoplasma solani’ using multilocus sequence typing analysis

“…The relatively low percentage of samples amplified for the stamp and secY genes ($60%) confirmed the high genetic variability that has been reported in previous studies on vmp1 Murolo et al, 2010Murolo et al, , 2013 …”

“…Conversely, a wider distribution of 'Ca. P. solani' tuf-type b has been reported for the regions of southern and central Italy (Pacifico et al, 2007;Pasquini et al, 2007;Murolo et al, 2010). This finding can be linked to the different compositions of the weeds around and within the vineyards, as locations with more rain and higher organic matter content in the soil favour nettle growth, which is the main host plant for tuf-type a (Maixner, 2011).…”

“…In the Marche region, where the present study was based, and where nettle is rarely found around vineyards, the BN-infected grapevines showed mainly ($80%) 'Ca. P. solani' tuf-type b (Murolo et al, 2010). The random presence of grapevines in the study vineyard that were infected by tuf-type a, which was not confined to the borders, indicated that the phytoplasma might have already been present in the propagation material.…”

“…The phylogenetic analysis of the vmp1 gene confirmed the results obtained in our previous study using RFLP analysis (Murolo et al, 2014), thus showing the accuracy of this technique. However, RFLP is a preliminary tool for the estimation of genetic diversity, and it requires the support of a more informative tool, such as sequence analysis Papura et al, 2009;Murolo et al, 2010;Foissac et al, 2013). In the phylogenetic trees of vmp1, stamp, and secY, and independent from the genes analysed, we recorded a robust correlation between tuf characterisation and the isolation of a branch that clustered the isolates characterised as tuf-type a, as already demonstrated in previous studies (Fabre et al, 2011;Cvrković et al, 2014;Kostadinovska et al, 2014).…”

The molecular epidemiology of bois noir grapevine yellows caused by ‘Candidatus Phytoplasma solani’ in the Republic of Macedonia

“…1). All the detected vmp1 profiles were previously published and designated with these names (Murolo et al 2010(Murolo et al , 2013Cvrković et al 2014).…”