Genetic diversity of European phytoplasmas of the 16SrV taxonomic group and proposal of ‘Candidatus Phytoplasma rubi’

Abstract

2CRA -Centro di ricerca per la viticoltura, 26 viale XXVIII Aprile 31015, Conegliano (TV), ItalyIn addition to the grapevine flavescence doré e phytoplasmas, other members of taxonomic group 16SrV phytoplasmas infect grapevines, alders and species of the genera Clematis and Rubus in Europe. In order to investigate which phytoplasmas constitute discrete, species-level taxa, several strains were analysed by comparing their 16S rRNA gene sequences and a set of five housekeeping genes. Whereas 16S rRNA gene sequence similarity values were .97.5 %, the proposed threshold to distinguish two 'Candidatus Phytoplasma' taxa, phylogenetic analysis of the combined sequences of the tuf, rplV-rpsC, rplF-rplR, map and uvrB-degV genetic loci showed that two discrete phylogenetic clusters could be clearly distinguished. The first cluster grouped flavescence doré e (FD) phytoplasmas, alder yellows (AldY) phytoplasmas, Clematis (CL) phytoplasmas and the Palatinate grapevine yellows (PGY) phytoplasmas. The second cluster comprised Rubus stunt (RS) phytoplasmas. In addition to the specificity of the insect vector, the Rubus stunt phytoplasma contained specific sequences in the 16S rRNA gene. Hence, the Rubus stunt phytoplasma 16S rRNA gene was sufficiently differentiated to represent a novel putative taxon: 'Candidatus Phytoplasma rubi'.Phytoplasmas are plant-pathogenic bacteria belonging to the class Mollicutes, a group of cell wall-less microorganisms phylogenetically related to Gram-positive bacteria with a low DNA G+C content (Weisburg et al., 1989). Phytoplasmas are still unavailable in culture. They are responsible for hundreds of crop diseases worldwide (Lee et al., 2000) and are transmitted from plant to plant by sap-sucking hemipteran insects (Weintraub & Beanland, 2006). Flavescence dorée (FD) of grapevine, a quarantine disease first reported in the 1950s in south-western France (Caudwell, 1957) is now present in southern Europe (Batlle et al., 1997;Belli et al., 1985;Boudon-Padieu, 2002;Duduk et al., 2003). The causal agent of FD was shown to be a phytoplasma (Caudwell et al., 1971) that is transmitted by a grapevine leafhopper of north American origin, Scaphoideus titanus (Ball.) (Schvester et al., 1961). The FD phytoplasma belongs to the 16SrV taxonomic group (Lee et al., 1998). Members of this group share high 16S rRNA gene sequence similarity (Davis & Dally, 2001), but the group consists of phytoplasmas with an important variety of biological niches restricted to woody perennial hosts. 'Candidatus P. ulmi' in the 16SrV-A subgroup is responsible for yellows of elm species in North America and Europe (Lee et al., 2004) and 'Candidatus P. ziziphi' in the 16SrV-B subgroup is the agent of jujube witches'-broom and cherry lethal yellows in Asia (Jung et al., 2003;Lee et al., 2004). In Europe, other phytoplasmas in the 16SrV group mainly infect grapevines (Maixner et al., 1994), alder (Lederer & Seemüller, 1991; Mäurer et al., 1993), blackberry (de Fluiter & van der Meer, 1953; Mäurer & Seemüller, 1995), species of the genu...

Phytoplasmas and Phytoplasma Diseases: A Severe Threat to Agriculture

“…P. rubi" AY197648 [172] V-F Balanite witches' broom (BltWB) 'Ca. P. balanitae' AB689678 [173] 16SrVI: Clover proliferation (Europe, America, Asia)…”

‘ Candidatus Phytoplasma solani’, a novel taxon associated with stolbur- and bois noir-related diseases of plants

“…However, according to IRPCM guidelines (IRPCM Phytoplasma/Spiroplasma Working TeamPhytoplasma Taxonomy Group, 2004), phytoplasmas sharing .97.5 % 16S rRNA gene nucleotide sequence similarity can be described as separate species if they are clearly distinguished by evident molecular diversity and ecological niche. These latter criteria were previously employed for delineating 'Candidatus Phytoplasma ulmi', 'Candidatus Phytoplasma rubi', 'Candidatus Phytoplasma mali', 'Candidatus Phytoplasma prunorum' and 'Candidatus Phytoplasma pyri' (Lee et al, 2004;Malembic-Maher et al, 2011;Seemüller & Schneider, 2004).…”

First report on molecular detection of a stolbur phytoplasma (Group16SrXII-A) associated with kenaf (Hibiscus cannabinusL.) in India

“…tuf, rpsC-rplV, rplF-rplR, map-SecY, and uvrB-degV (Malembic-Maher et al 2011). PCR conditions for this assay were optimised to ensure the sensitive detection of phytoplasma subgroup.…”