Genetic Diversity and Geographical Distribution of Phytoplasmas Associated with Potato Purple Top Disease in Mexico

Insect Vector and Reservoir Plant of 'Fragaria × ananassa' Phyllody Phytoplasma (16SrXIII-F) in Central Region of Chile

Strawberry phyllody has emerged as a prevalent disease affecting Chilean strawberry in recent years. The causal pathogen, 'Fragaria × ananassa' phyllody phytoplasma (StrPh), is categorized within the 16S ribosomal group XIII that is exclusively found in the Americas. In the context of economically significant crops, hemipteran insect vectors and alternative host plants play a pivotal role in their natural dissemination. This study comprehensively examined the key epidemiological facets of StrPh in the central region of Chile: the insect vector and alternative hosts. Through field surveys, we identified an abundance of an insect species, Cixiosoma sp., in an StrPh-infected strawberry field and confirmed its role as a vector of this phytoplasma through subsequent transmission assays. Moreover, we found a spontaneous weed species, Galega officinalis, to be infected with StrPh, raising the possibility of it being a potential alternative host plant for this phytoplasma. StrPh was also detected in cold-stored strawberry runners purchased from a nursery that supplies the local strawberry cultivation, suggesting a potential source of this phytoplasma in Chile. Collectively, these findings provide a significant epidemiological source of StrPh dissemination in central Chile.

Improving the Comprehension of Pathogenicity and Phylogeny in 'Candidatus Phytoplasma meliae' through Genome Characterization

'Candidatus Phytoplasma meliae' is a pathogen associated with chinaberry yellowing disease, which has become a major phytosanitary problem for chinaberry forestry production in Argentina. Despite its economic impact, no genome information of this phytoplasma has been published, which has hindered its characterization at the genomic level. In this study, we used a metagenomics approach to analyze the draft genome of the 'Ca. P. meliae' strain ChTYXIII. The draft assembly consisted of twenty-one contigs with a total length of 751.949 bp, and annotation revealed 669 CDSs, 34 tRNAs, and 1 set of rRNA operons. The metabolic pathways analysis showed that ChTYXIII contains the complete core genes for glycolysis and a functional Sec system for protein translocation. Our phylogenomic analysis based on 133 single-copy genes and genome-to-genome metrics supports the classification as unique 'Ca. P. species' within the MPV clade. We also identified 31 putative effectors, including a homolog to SAP11 and others that have only been described in this pathogen. Our ortholog analysis revealed 37 PMU core genes in the genome of 'Ca. P. meliae' ChTYXIII, leading to the identification of 2 intact PMUs. Our work provides important genomic information for 'Ca. P. meliae' and others phytoplasmas for the 16SrXIII (MPV) group.

Cas12a-Based Diagnostics for Potato Purple Top Disease Complex Associated with Infection by 'Candidatus Phytoplasma trifolii'-Related Strains

'Candidatus Phytoplasma trifolii' is a cell wall-less phytopathogenic bacterium that infects many agriculturally important plant species such as alfalfa, clover, eggplant, pepper, potato, and tomato. The phytoplasma is responsible for repeated outbreaks of potato purple top (PPT) and potato witches' broom (PWB) that occurred along the Pacific Coast of the United States since 2002, inflicting significant economic losses. To effectively manage these phytoplasmal diseases, it is important to develop diagnostic tools for specific, sensitive, and rapid detection of the pathogens. Here we report the development of a DNA endonuclease targeted CRISPR trans reporter (DETECTR) assay that couples isothermal amplification and Cas12a transcleavage of fluorescent oligonucleotide reporter for highly sensitive and specific detection of 'Candidatus Phytoplasma trifolii'-related strains responsible for PPT and PWB. The DETECTR assay was capable of specifically detecting the 16S-23S ribosomal DNA intergenic transcribed spacer sequences from PPT- and PWB-diseased samples at the attomolar sensitivity level. Furthermore, the DETECTR strategy allows flexibility to capture assay outputs with fluorescent microplate readers or lateral flow assays for potentially high-throughput and/or field-deployable disease diagnostics.

Plants and Phytoplasmas: When Bacteria Modify Plants

Plant pathogen presence is very dangerous for agricultural ecosystems and causes huge economic losses. Phytoplasmas are insect-transmitted wall-less bacteria living in plants, only in the phloem tissues and in the emolymph of their insect vectors. They are able to manipulate several metabolic pathways of their hosts, very often without impairing their life. The molecular diversity described (49 'Candidatus Phytoplasma' species and about 300 ribosomal subgroups) is only in some cases related to their associated symptomatology. As for the other plant pathogens, it is necessary to verify their identity and recognize the symptoms associated with their presence to appropriately manage the diseases. However, the never-ending mechanism of patho-adaptation and the copresence of other pathogens makes this management difficult. Reducing the huge impact of phytoplasma-associated diseases in all the main crops and wild species is, however, relevant, in order to reduce their effects that are jeopardizing plant biodiversity.

Survey for 'Candidatus Liberibacter' and 'Candidatus Phytoplasma' in Citrus in Chile

The considerable economic losses in citrus associated with ‘Candidatus Liberibacter’ and ‘Candidatus Phytoplasma’ presence have alerted all producing regions of the world. In Chile, none of these bacteria have been reported in citrus species. During the years 2017 and 2019, 258 samples presenting symptoms similar to those associated with the presence of these bacteria were examined. No detection of ‘Ca. Liberibacter’ associated with “huanglongbing” disease was obtained in the tested samples; therefore, this quarantine pest is maintained as absent in Chile. However, 14 plants resulted positive for phytoplasmas enclosed in subgroups 16SrV-A (12 plants) and 16SrXIII-F (2 plants). Although they have been found in other plant species, this is the first report of these phytoplasmas in citrus worldwide.

Identification of Phytoplasmas Representing Multiple New Genetic Lineages from Phloem-Feeding Leafhoppers Highlights the Diversity of Phytoplasmas and Their Potential Vectors

Phytoplasmas are obligate transkingdom bacterial parasites that infect a variety of plant species and replicate in phloem-feeding insects in the order Hemiptera, mainly leafhoppers (Cicadellidae). The insect capacity in acquisition, transmission, survival, and host range directly determines the epidemiology of phytoplasmas. However, due to the difficulty of insect sampling and the lack of follow-up transmission trials, the confirmed phytoplasma insect hosts are still limited compared with the identified plant hosts. Recently, quantitative polymerase chain reaction (qPCR)-based quick screening of 227 leafhoppers collected in natural habitats unveiled the presence of previously unknown phytoplasmas in six samples. In the present study, 76 leafhoppers, including the six prescreened positive samples, were further examined to identify and characterize the phytoplasma strains by semi-nested PCR. A total of ten phytoplasma strains were identified in leafhoppers from four countries including South Africa, Kyrgyzstan, Australia, and China. Based on virtual restriction fragment length polymorphism (RFLP) analysis, these ten phytoplasma strains were classified into four distinct ribosomal (16Sr) groups (16SrI, 16SrIII, 16SrXIV, and 16SrXV), representing five new subgroups (16SrI-AO, 16SrXIV-D, 16SrXIV-E, 16SrXIV-F, and 16SrXV-C). The results strongly suggest that the newly identified phytoplasma strains not only represent new genetic subgroup lineages, but also extend previously undiscovered geographical distributions. In addition, ten phytoplasma-harboring leafhoppers belonged to seven known leafhopper species, none of which were previously reported insect vectors of phytoplasmas. The findings from this study provide fresh insight into genetic diversity, geographical distribution, and insect host range of phytoplasmas. Further transmission trials and screening of new potential host plants and weed reservoirs in areas adjacent to collection sites of phytoplasma harboring leafhoppers will contribute to a better understanding of phytoplasma transmission and epidemiology.

List of non-EU phytoplasmas of tuber-forming Solanum spp

Following a request from the European Commission, the EFSA Panel on Plant Health prepared a list of non-EU phytoplasmas of tuber-forming Solanum spp. A systematic literature review and search of databases identified 12 phytoplasmas infecting S. tuberosum. These phytoplasmas were assigned to three categories. The first group (a) consists of seven non-EU phytoplasmas, known to occur only outside the EU ('Candidatus Phytoplasma americanum', 'Ca. P. australiense', 'Ca. P. fragariae'-related strain (YN-169, YN-10G) and 'Ca. P. hispanicum') or having only limited presence in the EU ('Ca. P. aurantifolia'-related strains, 'Ca. P. pruni'-related strains and 'Ca. P. trifolii'). The second group (b) consists of three phytoplasmas originally described or reported from the EU. The third group (c) consists of two phytoplasmas with substantial presence in the EU, whose presence in S. tuberosum is not fully supported by the available literature. Phytoplasmas of categories (b) and (c) were excluded at this stage from further categorisation efforts. Three phytoplasmas from category (a) ('Ca. P. australiense', 'Ca. P. hispanicum' and 'Ca. P. trifolii') were excluded from further categorisation, as a pest categorisation has already been performed by EFSA. Comments provided by the EU Member States were integrated in the opinion. The main uncertainties of this listing concern: the taxonomy, the geographic distribution and prevalence and host range. The following phytoplasmas considered as non-EU and whose presence in S. tuberosum is fully supported by literature (category (a)) are categorised by the Panel in a separate opinion: 'Ca. P. americanum', 'Ca. P. fragariae'-related strain (YN-169, YN-10G), 'Ca. P. aurantifolia'-related strains and 'Ca. P. pruni'-related strains.

Pest categorisation of the non-EU phytoplasmas of tuber-forming Solanum spp

Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of four phytoplasmas of tuber-forming Solanum spp. known to occur only outside the EU or having a limited presence in the EU. The only tuber-forming species of Solanum reported to be phytoplasma infected is S. tuberosum. This opinion covers 'Candidatus Phytoplasma americanum', 'Ca. P. aurantifolia'-related strains (GD32; St_JO_10, 14, 17; PPT-SA; Rus-343F; PPT-GTO29, -GTO30, -SINTV; Potato Huayao Survey 2; Potato hair sprouts), 'Ca. P. fragariae'-related strains (YN-169, YN-10G) and 'Ca. P. pruni'-related strains (Clover yellow edge; Potato purple top AKpot7, MT117, AKpot6; PPT-COAHP, -GTOP). Phytoplasmas can be detected by molecular methods and are efficiently transmitted by vegetative propagation. Phytoplasmas are also transmitted in a persistent and propagative manner by some insects belonging to families within Cicadomorpha, Fulgoromorpha and Sternorrhyncha (order Hemiptera). No transovarial, pollen or seed transmission has been reported. The reported natural host range of the phytoplasmas categorised here varies from restricted ('Ca. P. americanum', and 'Ca. P. fragariae'-related strains) to wide ('Ca. P. aurantifolia'-related strains and 'Ca. P. pruni'-related strains), thus increasing the possible entry pathways in the latter case. S. tuberosum is widely cultivated in the EU. All the categorised phytoplasmas can enter and spread through the trade of host plants for planting, and by vectors. Establishment of these phytoplasmas is not expected to be limited by EU environmental conditions. The introduction of these phytoplasmas in the EU would have an economic impact. There are measures to reduce the risk of entry, establishment, spread and impact. Uncertainties result from limited information on distribution, biology and epidemiology. All the phytoplasmas categorised here meet the criteria evaluated by EFSA to qualify as potential Union quarantine pests, and they do not meet all the criteria to qualify as potential regulated non-quarantine pests, because they do not occur or are not known to be widespread in the EU.

Pest categorisation of the non-EU phytoplasmas of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L

Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of nine phytoplasmas of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. (hereafter “host plants”) known to occur only outside the EU or having a limited presence in the EU. This opinion covers the (i) reference strains of ‘Candidatus Phytoplasma australiense’, ‘Ca. P. fraxini’, ‘Ca. P. hispanicum’, ‘Ca. P. trifolii’, ‘Ca. P. ziziphi’, (ii) related strains infecting the host plants of ‘Ca. P. aurantifolia’, ‘Ca. P. pruni’, and ‘Ca. P. pyri’, and (iii) an unclassified phytoplasma causing Buckland valley grapevine yellows. Phytoplasmas can be detected by available methods and are efficiently transmitted by vegetative propagation, with plants for planting acting as a major entry pathway and a long‐distance spread mechanism. Phytoplasmas are also transmitted in a persistent and propagative manner by some insect families of the Fulgoromorpha, Cicadomorpha and Sternorrhyncha (order Hemiptera). No transovarial, pollen or seed transmission has been reported. The natural host range of the categorised phytoplasmas varies from one to more than 90 plant species, thus increasing the possible entry pathways. The host plants are widely cultivated in the EU. All the categorised phytoplasmas can enter and spread through the trade of host plants for planting, and by vectors. Establishment of these phytoplasmas is not expected to be limited by EU environmental conditions. The introduction of these phytoplasmas in the EU would have an economic impact. There are measures to reduce the risk of entry, establishment, spread and impact. Uncertainties result from limited information on distribution, biology and epidemiology. All the phytoplasmas categorised here meet the criteria evaluated by EFSA to qualify as potential Union quarantine pests, and they do not qualify as potential regulated non‐quarantine pests, because they are non‐EU phytoplasmas.

Global Status of Phytoplasma Diseases in Vegetable Crops

The presence of phytoplasmas and their associated diseases is an emerging threat to vegetable production which leads to severe yield losses worldwide. Phytoplasmas are phloem-limited pleomorphic bacteria lacking the cell wall, mainly transmitted through leafhoppers but also by plant propagation materials and seeds. Phytoplasma diseases of vegetable crops are characterized by symptoms such as little leaves, phyllody, flower virescence, big buds, and witches' brooms. Phytoplasmas enclosed in at least sixteen different ribosomal groups infecting vegetable crops have been reported thus far across the world. The aster yellows phytoplasma group (16SrI) is presently the prevalent, followed by the peanut witches' broom (16SrII). Wide and overlapping crop and non-crop host ranges of phytoplasmas, polyphagous insect vectors, limited availability of resistance sources and unavailability of environmentally safe chemical control measures lead to an arduous effort in the management of these diseases. The most feasible control of vegetable phytoplasma diseases is a consequence of the development and implementation of integrated disease management programs. The availability of molecular tools for phytoplasma identification at the strain level greatly facilitated this kind of approach. It is moreover essential to understand the molecular basis of phytoplasma-vector interaction, epidemiology and other factors involved in disease development in order to reduce the disease outbreaks. Information on the knowledge about the most widespread phytoplasma diseases in vegetable crops is reviewed here in a comprehensive manner.

Potato purple top disease associated with the novel subgroup 16SrII-X phytoplasma

Potato (Solanum tuberosum) is a very economically important perennial tuberous crop in Saudi Arabia. Potato plants displaying symptoms associated with potato purple top disease, such as aerial tubers and purple and small leaves, were observed in Al-Bukairiyah, Fowlq and Buraydah, Al-Tarafiyah, Qassim governorate, Saudi Arabia. In this study, we examined samples taken from 12 symptomatic potato plants and confirmed the presence of phytoplasma DNA. Analysis of the 16S rRNA-encoding sequences revealed that the symptomatic plants were infected with phytoplasma belonging to the peanut witches'-broom group (16SrII). Sequencing of the 16S rRNA- encoding gene, computer-simulated RFLP analysis and phylogenetic analysis revealed the presence of a novel representative of the 16SrII-X subgroup. The present study identified potato plants as a novel host for novel phytoplasma strains belonging to the pigeon pea witches'-broom group in Saudi Arabia.

Identification of a 'Candidatus Phytoplasma hispanicum'-related strain, associated with yellows-type diseases, in smoke-tree sharpshooter (Homalodisca liturata Ball)

The 16SrXIII group from phytoplasma bacteria were identified in salivary glands from Homalodisca liturata, which were collected in El Comitán on the Baja California peninsula in Mexico. We were able to positively identify 15 16S rRNA gene sequences with the corresponding signature sequence of 'CandidatusPhytoplasma' (CAAGAYBATKATGTKTAGCYGGDCT) and in silico restriction fragment length polymorphism (RFLP) profiles (F value estimations) coupled with a phylogenetic analysis to confirm their relatedness to 'CandidatusPhytoplasma hispanicum', which in turn belongs to the 16SrXIII group. A restriction analysis was carried out with AluI and EcoRI to confirm that the five sequences belongs to subgroup D. The rest of the sequences did not exhibit any known RFLP profile related to a subgroup reported in the 16SrXIII group.

Delineation of a novel subgroup 16SrXIII-J phytoplasma, a 'Candidatus Phytoplasma hispanicum'-related strain, based on computer-simulated RFLP and phylogenetic analysis

Symptoms of fruit phyllody and slow growth, which are suggestive of phytoplasma infection, were observed in strawberry plants cultivated in commercial fields. In order to provide evidence of association of phytoplasma with affected plants, assays for detecting and identifying were performed through computer-simulated restriction fragment length polymorphism (RFLP) and phylogenetic analysis. Total DNA was extracted from symptomatic and asymptomatic samples and used as template in nested PCR primed by the primers P1/Tint followed by R16F2n/16R2. Amplified DNA fragments of 1.2 kb from the 16S rRNA gene revealed the presence of phytoplasma in all symptomatic samples. Molecular detection was confirmed by electron transmission microscopy, which evidenced pleomorphic bodies in the phloem vessels. Nucleotide sequence representative of the strawberry phytoplasma shared 97.2 to 99 % similarity with phytoplasmas currently classified as members of the distinct subgroups within the 16SrXIII group. Similarity coefficient (F) values ranged from 0.70 to 0.92, indicating that strawberry phytoplasma delineates a new strain in addition to 'Candidatus Phytoplasma hispanicum'-related strains. The evolutionary tree displayed that this strain emerges as a new branch in relation to those previously described. The novel strain, designated SFP (strawberry fruit phyllody) phytoplasma represents the new 16SrXIII-J subgroup and its sequence, denominated SFP-Br02, was deposited in the GenBank database (EU719108). These findings contribute for the knowledge of the genetic diversity existing among members of the group 16SrXIII and establishes strawberry as an additional host of representatives of this group in Brazil.

Molecular diagnostic assays based on cpn60 UT sequences reveal the geographic distribution of subgroup 16SrXIII-(A/I)I phytoplasma in Mexico

Geographically diverse samples from strawberry exhibiting symptoms of Strawberry Green Petal (SbGP), periwinkle plants with virescence, and blackberry, blueberry, and raspberry plants displaying yellowing and inedible fruits, were assayed for the presence of phytoplasma DNA. PCR targeting the 16S rRNA-encoding gene and chaperonin-60 (cpn60) showed that the plants were infected with phytoplasma subgroup16SrXIII-(A/I)I (SbGP/MPV). To examine the geographic distribution of this pathogen in Mexico, we designed an array of cpn60-targeted molecular diagnostic assays for SbGP/MPV phytoplasma. A fluorescent microsphere hybridization assay was designed that was capable of detecting SbGP/MPV phytoplasma in infected plant tissues, successfully differentiating it from other known phytoplasma cpn60 UT sequences, while identifying a double infection with SbGP/MPV and aster yellows (16SrI) phytoplasma. Two quantitative assays, quantitative real-time PCR (qRT-PCR) and droplet digital PCR (ddPCR), gave similar results in infected samples. Finally, a loop-mediated isothermal amplification (LAMP) assay provided rapid detection of SbGP/MPV phytoplasma DNA. Application of these assays revealed that SbGP/MPV phytoplasma is widely distributed in Central Mexico, with positive samples identified from eleven localities within three states separated by hundreds of kilometres. These results also provide tools for determining the presence and geographic distribution of this pathogen in plant and insect samples in other localities.

Diagnosis of Phytoplasmas by Real-Time PCR Using Locked Nucleic Acid (LNA) Probes

Phytoplasma infections are regularly reported worldwide, and concerns about their threats on agricultural production, especially in relation to global climate change, are increasing. Sensitive and reliable detection methods are important to ensure that propagation material is free of phytoplasma infection and for epidemiological studies that may provide information to limit the extent of phytoplasma diseases and to prevent large-scale crop losses. The detection method described here uses LNA chemistry in real-time PCR. It has been developed and validated for use on potatoes, and its sensitivity and specificity make it suitable for use in postentry potato quarantine and initiation of potato nuclear stocks to ensure that material is phytoplasma-free.

Detection and identification of a novel 16SrXIII subgroup phytoplasma associated with strawberry red leaf disease in Argentina

Strawberry red leaf phytoplasma was found in strawberry plants from production fields in Lules (Tucumán province) and Bella Vista (Corrientes province), Argentina. Characteristic strawberry red leaf symptoms were stunting, young leaves with yellowing at the edges, mature leaves which curled and were reddish at the abaxial face, flower and fruit deformation and death. The pathogen was detected with phytoplasma-universal primer pairs P1/P7 followed by R16F2n/R16R2 as nested primers in 13 diseased plants. Based on RFLP and sequence analysis of the amplified 16S rRNA gene, the phytoplasma was related to the 16SrXIII group (Mexican periwinkle virescence). In silico the RFLP profile of all the samples analysed revealed the presence of a unique pattern, showing that the novel phytoplasma is different from all the phytoplasmas currently composing the 16SrXIII group. The phylogenetic analysis was consistent with RFLP analysis as the strawberry red leaf phytoplasma was grouped within the 16SrXIII group, but formed a particular cluster. On this basis, the Strawberry red leaf phytoplasma associated with strawberry red leaf disease was assigned to a new subgroup, 16SrXIII-F.

Association of "Candidatus Liberibacter solanacearum" with the psyllid, Trioza apicalis (Hemiptera: Triozidae) in Europe

The psyllid Trioza apicalis Förster (Hemiptera: Triozidae) is a serious pest of carrots, Daucus carota L., in Europe. Carrots exhibiting symptoms of psyllid damage were observed in commercial fields in southern Finland in 2008. Symptoms in affected plants included leaf curling, yellow and purple discoloration of leaves, stunted growth of shoots and roots, and proliferation of secondary roots. Mechanisms by which T. apicalis induces symptoms in plants are not understood, and no plant pathogens have yet been associated with this insect. Given recent association of liberibacter with several crops affected by psyllids, an investigation on whether this bacterium is associated with T. apicalis was conducted. Polymerase chain reaction (PCR) primer pairs OA2/OI2c and LsoF/OI2c, specific for 16S rRNA gene from "Candidatus Liberibacter solanacearum," generated amplicons of 1,168 bp and 1,173 bp, respectively, from DNA extracted from field-collected psyllids (61 and 36.6%, respectively), laboratory-reared psyllids (70 and 33.3%, respectively), field-collected petioles from symptomatic carrots (80 and 55%, respectively), and laboratory-grown carrots (100% for both primer pairs). In contrast, no PCR products were detected in DNA extracted from insect-free plants. The DNA sequences of amplicons of the genes encoding liberibacter 16S rRNA from psyllids and carrots were identical. DNA of the 16S rRNA gene sequences determined from carrots and psyllids were 99.9% identical to analogous sequences of "Ca. L. solanacearum" amplified from several solanaceous crops and the psyllid Bactericera cockerelli (Sulc), a vector of this bacterium. This is the first report of a plant pathogen associated with T. apicalis and the second known psyllid species associated with "Ca. L. solanacearum".