Genetic variation, phylogenetic relationship and spatial distribution of ‘Candidatus Phytoplasma ulmi’ strains in Germany

Abstract

A recent survey in Germany revealed the wide presence of ‘Candidatus Phytoplasma ulmi’ in native elm stands. Accessions were studied for their genetic variability and phylogenetic relationship based on the conserved groEL and the variable imp gene. While the groEL sequences revealed a high intraspecific homology of more than 99%, the homology of the imp gene dropped to 71% between distantly related sequences. Twenty-nine groEL and 74 imp genotypes were distinguished based on polymorphic sites. Phylogenetic analysis of the groEL gene clustered all ‘Ca. P. ulmi’ strains and separated them from related phytoplasmas of the 16SrV group. The inferred phylogeny of the imp gene resulted in a different tree topology and separated the ‘Ca. P. ulmi’ genotypes into two clusters, one closely related to the flavescence dorée phytoplasma strain FD-D (16SrV-D), the other affiliated with the flavescence dorée phytoplasma strains FD-C and FD70 and the alder yellows phytoplasma (16SrV-C). In both phylograms, ‘Ca. P. ulmi’ genotypes from Scots elm trees formed a coherent cluster, while genotypes from European white elms and field elms grouped less strictly. The regional distribution pattern was congruent for some of the groEL and imp genotypes, but a strict linkage for all genotypes was not apparent.

Occurrence, Impact, and Multilocus Sequence Analysis of Alder Yellows Phytoplasma Infecting Common Alder and Italian Alder in Southern Italy

“…The occurrence of a wide array of different map genotypes in alder trees in southern Italy further supports data of previous investigations by which a higher diversity of the mentioned genotypes was found in alder trees and O. alni than in grapevine and S. titanus, all sampled in various areas of five European countries [24]. Prior to this work, only one and two ALY strains had been examined at imp and groEL gene sequence level, respectively [9,50]. On the other hand, sequence and phylogenetic analyses of both genes have been widely used to characterize and differentiate strains of 'Ca.…”

“…Sequence analysis of imp gene of 25 NR-SI-ALY strains showed similarity values which varied from 70.2% (ALY2453 versus ALY2603) to 100% (ALY2462 versus ALY2606) ( Table S10 ). The most closely related to NR-SI-ALY strains was the strain ALY1, previously recorded in A. glutinosa in Germany [ 50 ], which shared 72.1–99.8% imp gene sequence similarity with them. NR-SI-ALY strains shared 71–99.6% imp gene sequence similarity with FD strains (CH, FD-D, FD-C-Piemonte, and FD70) and were more distantly related to EY strains, sharing with them 67.3–90.8% imp gene sequence similarity.…”

“…At groEL gene sequence level, NR-SI-ALY strains showed similarity values ranging from 98.2% (ALY2453 versus ALY2462) to 100% (ALY2588 versus ALY3016) ( Table S11 ). NR-SI-ALY strains shared 97.7–99.1% and 97.3–98% groEL gene sequence similarity with the periwinkle-maintained ALY strain [ 50 ] and the strain AldY-WA1, respectively. Other 16SrV group members which were most closely related to NR-SI-ALY strains, were FD-(CH) and FD-(FD70), and EY-(JB0071-C04-CFIA7-2) and EY-(4120-Ul-SN), sharing with them 98–99.5% and 98.3–99.3% groEL gene sequence similarity, respectively.…”

“…titanus , all sampled in various areas of five European countries [ 24 ]. Prior to this work, only one and two ALY strains had been examined at imp and groEL gene sequence level, respectively [ 9 , 50 ]. On the other hand, sequence and phylogenetic analyses of both genes have been widely used to characterize and differentiate strains of ‘ Ca .…”

“…Both primer pairs are specific for the EY-group phytoplasmas. Imp gene, which encodes an immunodominant surface protein, and groEL gene encoding the heat-shock protein GroEL, were amplified through the EY group-specific primer pairs fEY_imp/rpyrG and fEY_groEL/rEY_groEL, respectively [ 50 ]. Primer pair fEY_imp/rpyrG yielded a 675 bp DNA fragment, whereas primer pair fEY_groEL/rEY_groEL amplified a fragment of about 880 bp in length.…”