Costanzo, Stefano

In the fall of 2015 and 2016, during annual disease surveys conducted by the Pennsylvania Department of Agriculture, seven peach trees (Prunus persica) from a commercial orchard in Berks County, PA, were observed exhibiting symptoms consistent with phytoplasma infection. Symptoms included premature leaf yellowing and reddening, foliar epinasty, shotholes and vein reddening. Seven out of 700 peach trees in the orchard displayed these symptoms and were ultimately removed. Leaf and stem samples were collected from seven symptomatic trees as well as from five asymptomatic ones for further analysis. Total DNA was extracted using the Qiagen DNeasy Plant Kit. All DNA samples were initially screened using a phytoplasma-specific real-time PCR assay (Hodgetts et al., 2009). Phytoplasma was detected in all symptomatic plants, but in none of the five asymptomatic plants. Positive samples were subsequently used in conventional nested PCR targeting the 16S rRNA gene, using primer pairs P1/16S-SR followed by P1A/16S-SR (Deng & Hiruki, 1991; Lee et al., 2004). PCR products were cloned, and sequenced. Four representative sequences were deposited in GenBank under accession numbers PV770936 to PV770939. Sequence analysis using BLASTn (NCBI) and iPhyClassifier (Zhao et al., 2009) revealed that the phytoplasma strains, designated as PYP-PA03, 04, 06, and 07, shared between 97.5% (1,482/1,520 bp) and 97.63% (1,483/1519 bp) sequence identity with the ‘Candidatus Phytoplasma fraxini’ reference strain 16SrVII-A (AF092209), suggesting that the peach associated phytoplasma is a ‘Ca. P. fraxini’-related strain. However, virtual RFLP analysis of the 16S rDNA F2nR2 fragments revealed patterns distinct from all previously established 16Sr groups/subgroups. The closest similarity was observed with members of the 16Sr group VI, but similarity coefficients were below the accepted subgroup threshold (0.97), supporting the distinctiveness of these strains. To further characterize the PYP-PA phytoplasma, partial sequences of the tuf and secA genes were PCR-amplified, cloned, and sequenced following protocols by Makarova et al. (2012) and Dickinson & Hodgetts (2013). The resulting sequences were identical for each gene, and one sequence was deposited in GenBank under accession numbers PV769898 (tuf gene) and PV769899 (secA gene). BLASTn analysis of the tuf gene revealed 93.25% (470/504 bp) and 90.67% (457/504 bp) sequence identity with the homologous gene in the Argentinian alfalfa witches’-broom phytoplasma isolate ArAWB-2021 16SrVII-C (CP131022) and the ‘Ca. P. fraxini’ isolate AshY1 16SrVII-A (CP146843), respectively. Similarly, the secA gene shared 89.16% (691/775 bp) and 88.30% (679/769 bp) sequence identity with the same isolates ArAWB-2021 (CP131022) and AshY1 (CP146843), respectively. These collective results suggest that the PYP-PA phytoplasma is phylogenetically related to members of the Ash yellows group (16SrVII). In 2010, Zunnoon‐Khan et al. identified a phytoplasma strain PRU0430 of group 16SrVII associated with peach trees in Ontario, Canada (GU223903). To our knowledge, the present study is the first to report a ‘Ca. P. fraxini’-related strain associated with peach trees in the United States. These findings highlight the need for further research to fully characterize this potentially novel phytoplasma, which constitutes a distinct lineage from the one identified in Canada and underscore the importance of continued surveillance and molecular investigation of emerging phytoplasma-associated diseases in the region.

‘Candidatus Liberibacter asiaticus’ is the unculturable causative agent of citrus huanglongbing disease. Here, we report the first citrus root metagenome sequence containing the draft genome of ‘Ca. L. asiaticus’ strain AHCA17, obtained from a pummelo tree in California. The assembled genome was 1.2 Mbp and resulted in 37 contigs (N50 = 158.7 kbp) containing 1,057 predicted open reading frames and 45 RNA-coding genes. This draft genome will provide a valuable resource in further study of ‘Ca. L. asiaticus’ genome diversity and pathogen epidemiology.

AbstractIn order to devise a method for rapid detection of ‘Candidatus (Ca.) Phytoplasma pini’ and for distinguishing it rapidly from other phytoplasmas, we carried out preliminary sequencing of Lithuanian ‘Ca. Phytoplasma pini’ strain PineBL2 using Illumina (NGS) technology and targeted sequencing employing universal phytoplasma primers. We focused on two resulting chromosomal segments that contained a 16S rRNA gene and a translation elongation factor EF‐TU gene (tuf), respectively. Based on alignments of the ‘Ca. Phytoplasma pini’ gene sequences with the corresponding sequences of other phytoplasmas, we designed new primer pairs for PCR‐based detection of ‘Ca. Phytoplasma pini’. Because ‘Ca. Phytoplasma pini’ strains are expected to reside in the pine phloem in a very low titre, one might expect that they could be detected only by nested PCR. By contrast, the primers and PCR protocols designed in the current work enabled rapid direct PCR detection and identification of ‘Ca. Phytoplasma pini’ by amplifying a 484 bp 16S rDNA segment and a 513 bp tuf gene fragment that contain regions unique to this phytoplasma.