‘Candidatus Phytoplasma cirsii’, a novel taxon from creeping thistle [Cirsium arvense (L.) Scop.]

Abstract

Creeping thistle [Cirsium arvense (L.) Scop.] and dahlia (Dahlia sp.) plants showing typical symptoms of phytoplasma infection including yellowing, stunting, inflorescence and proliferation, were sampled; the presence of phytoplasma was confirmed by standard PCR using universal primers. RFLP analysis allowed classification of the detected phytoplasma strains CirYS, CirYS1 and DahlP within the 16SrXI group, the unique restriction profile F2nR2 fragment obtained in silico by iPhyClassifier indicated that they belong to the new 16SrXI-E subgroup. Genetic analysis of the 16S rRNA gene revealed that the studied strains shared less than 97.5 % similarity with all of the previously described 'Candidatus Phytoplasma' species. The closest relatives are 'Candidatus Phytoplasma cynodontis' and 'Candidatus Phytoplasma oryzae' with 96.8 % and 96.6 % similarity. All strains studied bear three specific regions in the 16S rRNA gene, discriminating them from the other phytoplasma species. Phylogenetic analysis of the 16S rRNA and secA genes confirmed this specificity, as the creeping thistle and dahlia phytoplasma strains clustered in a distinguishable lineage group. The uniqueness of the genetic analysis agrees with the biological characterization of the studied phytoplasma strains, their host range, and geographical distribution. The strains only infect dicotyledonous plants in Europe, contrary to their closest relatives. Based on their unique properties, it could be concluded that the studied phytoplasma strains represent a discrete group that is proposed as a novel taxon 'Candidatus Phytoplasma cirsii', with strain CirYS as a reference strain.Phytoplasmas are plant pathogens of the class Mollicutes, colonizing the phloem sieve of their host plants as well as the salivary glands and other organs of sap-sucking insect vectors. Phytoplasmas cause diseases on a broad scale and with a range of intensities of symptoms in more than 1000 plant species (Bertaccini, 2007). These non-helical wall-less bacteria are specialized strict parasites, characterized by the small reduced genome and the lack of several genes necessary for their independent metabolism. Apart from one partial success (Contaldo et al., 2012) they are not cultivable in vitro, which is one of the reasons that phytoplasmas are assigned into the provisional Candidatus genus status. Phytoplasma taxonomy is based on analysis of the variability of the 16S rRNA gene, and currently two systems are applied. The first system discriminates the phytoplasmas according to their random fragment length polymorphism (RFLP) variability and restriction endonuclease patterns into 16Sr groups and subgroups (Lee et al., 1998; Seemüller et al., 1998;Wei et al., 2007;Zhao et al., 2009b). Based on the recommendation of the IRPCM Phytoplasma/Spiroplasma Working Team-Phytoplasma Taxonomy Group (2004), the new and more precise 'Candidatus Phytoplasma' taxonomy system, reflecting the main taxonomic rule -the 97.5 % similarity of 16S rRNA gene sequences as a species border -is actually built. At ...

Revision of the ‘Candidatus Phytoplasma’ species description guidelines

“…It was described in the Czech Republic in association with yellowing, stunting and proliferation of creeping thistle and dahlia [50]. Two strains, including the reference strain CirYS (GenBank accession number KR869146), are available.…”

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

“…In 2007, based on the virtual RFLP analysis of all 16S rRNA gene sequences available at the time (F2nR2 fragment of about 1250 bp), the number of phytoplasma classification groups was expanded from 19 to 28 (16SrXIX-16SrXXVIII), and some potentially new species were proposed with suggested reference strains ( Table 3 ). In the present review, groups/subgroups corresponding to Candidatus Phytoplasma species, especially the newly named species are updated ( Table 3 [ 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 , 131 , 132 , 133 , 134 , 135 , 136 , 137 ]). Two new groups (16SrXXXVIII and 16SrXXXIX) are established based on the criterium which requires the collective F2nR2 RFLP pattern of any new group representative has a similarity coefficient of <0.85 with that of all previously recognized 16Sr groups [ 94 ] ( Supplementary Table S1 ).…”

Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas

“…Phytoplasma" species have been described (IRPCM, 2004;Kirdat et al, 2020;Naderali et al, 2017;Rodrigues Jardim et al, 2020;Šafářová et al, 2016;Zhao et al, 2021). Nevertheless, the phytoplasma lineage is a highly diverse monophyletic group (Gupta et al, 2018;Zhao et al, 2015), having been classified into 36 groups, and more than 150 subgroups based on distinct 16S rRNA gene restriction fragment length polymorphism patterns and sequencing (Lee et al, 1998;Naderali et al, 2017;Rodrigues Jardim et al, 2020;Seemüller et al, 1998;Wei et al, 2007;Zhao et al, 2009).…”