Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences

Abstract

The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy of these sequences for delineating phytoplasma strains within each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by secY gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on the secY gene permitted finer differentiation of phytoplasma strains, however. The secY gene-based phylogeny not only readily resolved 16Sr subgroups within a given 16Sr group, but also delineated distinct lineages irresolvable by 16S rRNA gene-based phylogeny. Such high resolving power makes the secY gene a more useful genetic marker than the 16S rRNA gene for finer differentiation of closely related phytoplasma strains based on RFLP analysis with selected restriction enzymes. Such strains were readily identified by collective secY RFLP patterns. The genetic interrelationships among these strains were determined by pattern similarity coefficients, which coincided with delineations by phylogenetic analysis. This study also revealed two heterogeneous spc operons present in the phytoplasma clade. This latter finding may have significant implications for phytoplasma evolution.

‘Candidatus Phytoplasma pruni’, a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes

“…Nucleotide sequence analyses revealed that the amplicons each contained a partial (39-end) rpl15 ribosomal protein (rp) gene, a complete secY gene, and a partial (59-end) map (methionine aminopeptidase) gene. Like various group 16SrIII phytoplasma strains and unlike some other phytoplasmas (Lee et al, 2010), the X-disease phytoplasma strains in this study lacked an adk (adenylate kinase) gene between the secY and map genes, a feature that marks a major evolutionary divergence among phytoplasma subclades. A 9-base insertion/deletion (indel) in the secY genomic locus distinguished two group 16SrIII phytoplasma strain clusters, one group containing strains having a secY gene length of 1263 bases (strains PX11CT1 R , PX11CT2, PX92CT1, PX92CT4, CX-95, WX95, WWB, PoiBI, SP1), and the other group containing strains having secY length of 1272 bases (strains CYE, MW1, GR1, PBT, PPTAKpot6, PPTAKpot7, PPTMT117, VAC) (Fig.…”

“…We also provide data on two additional genomic loci for the designated 'Ca. Phytoplasma pruni' reference strain PX11CT1 R , as well as for other strains, since improved delineation of species should be achieved through analyses of more variable gene sequences (Lee et al, 2010;Martini et al, 2007). Availability of nucleotide sequences from multiple genetic loci, such as those encoding SecY and ribosomal proteins, especially for the reference strain of a 'Ca.…”

“…conditions previously described (Lee et al, 2010;Martini et al, 2007). SecY genomic regions from strain CX-95 were amplified in direct hf-PCRs primed by primer pair SecYF1(III)/SecYR1(III).…”

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

“…PCR conditions and primers were as described by Gundersen et al (1996), Langer & Maixner (2004), Martini et al (2007) and Lee et al (2010). PCRproducts were cloned in plasmid vector pCRII-TOPO (Invitrogen) and propagated in Escherichia coli.…”

Maize bushy stunt phytoplasma affects native corn at high elevations in Southeast Mexico

“…Recently, other ribosomal and protein-encoding genes have been used to improve phytoplasma strain differentiation and/or to develop diagnostic methods (Lee et al 2010;Davis et al 2013;Dumonceaux et al 2014). The Cpn60-encoding gene has been successfully used as a marker for phytoplasma detection and differentiation (Mitrović et al 2011;Sugawara et al 2012;Alvarez et al 2014), and an approximately 550 bp portion of this gene, known as the chaperonin 60 universal target (cpn60UT) (Goh et al 1996) can be universally accessed and used to differentiate phytoplasmas (Pérez-López et al 2014;Dumonceaux et al 2014).…”