Weier Cui

Pear decline, caused by 'Candidatus Phytoplasma pyri', has emerged in Chilean pear orchards in recent years. While several Cacopsylla species are potential vectors of 'Ca. P. pyri', the disease's full epidemiological cycle remains uncertain. Cacopsylla bidens, present in Chilean orchards, has recently been reported as a vector. This study conducted year-long surveys in two commercial pear orchards across different Chilean regions, capturing C. bidens in zones with 'Ca. P. pyri'-infected pear trees. All developmental stages were collected, with peak abundances occurring in March and April. Outside the study zones, C. bidens were found in pine trees but not in adjacent cultivated areas. Two seasonal morphotypes, summer and winter forms, were identified. Molecular analysis detected 'Ca. P. pyri' in a high proportion of insects, with maximum infection rates in March and April. These findings advance our understanding of 'Ca. P. pyri' spatial and temporal dynamics and its potential role in 'Ca. P. pyri' spreading under Chilean field conditions.

Climate change is intensifying the simultaneous occurrence of biotic and abiotic stresses in fruit crops, but yet the molecular mechanisms underlying plant responses remain poorly understood. The physiological and transcriptomic responses of two sweet cherry (Prunus avium L.) cultivars, Santina and Bing, grafted onto Gisela 12, were investigated under single and combined stresses imposed by Pseudomonas syringae pv. syringae and water deficit. Although biomass, gas exchange, and hormone accumulation showed only minor changes, combined stress triggered distinct cultivar-dependent transcriptional reprogramming. The cultivar Bing exhibited a pronounced response with 4261 differentially expressed genes (DEGs), characterized by strong repression of photosynthetic processes and activation of defense- and hormone-related pathways. In contrast, the cultivar Santina showed a moderate response with 674 DEGs, primarily reinforcing structural and secondary metabolism. Cultivar-specific modulation of abscisic acid sensitivity was associated with the contrasting regulation of WRKY40 and Sin3-like repressors, despite comparable ABA levels. Strikingly, both cultivars upregulated the GIGANTEA gene, underscoring its role as a central regulatory hub linking circadian rhythm, stomatal function, and hormonal crosstalk under dual stress. Collectively, these results reveal non-additive, genotype-specific transcriptional strategies in sweet cherry trees, providing insights into stress integration in fruit trees and identifying regulatory genes that may inform breeding and management strategies for resilience under climate change.

‘ Candidatus Phytoplasma pyri’, the pathogen associated with pear decline, affects pear trees across both the old and new worlds. However, research on this phytoplasma has been limited by the lack of genomic data. This study presents the first draft genome of ‘ Ca. P. pyri’ using a strain from Chile, with its genomic features analyzed in comparison with the closely related ‘ Ca. Phytoplasma’ species ‘ Ca. P. mali’ and ‘ Ca. P. prunorum’. The draft genome spans 456,478 bp with a GC content of 20.4%. Key genes possibly associated with pathogenicity and potential pathogenic effectors were identified, and they are notably lacking orthologs of known effectors. A single potential mobile unit similar to that of ‘ Ca. P. mali’ was identified. It is characterized by the absence of the transposase tra5 and the presence of the IS3 family transposase iSErh1. Multilocus sequence analysis of six genetic markers (16S rRNA gene, LSU36p, tuf, aceF, secA, and secY) from 10 Chilean and 10 Italian samples revealed high genetic uniformity among the Chilean strains, collected from five geographically distant orchards over a span of 13 months; by contrast, strains with greater diversity were detected among those from Italy, collected from a few localities over approximately 30 years. These findings suggest limited evolutionary divergence of this phytoplasma in Chile. This study provides a foundational framework for investigations into the pathogenic mechanisms and evolutionary dynamics of ‘ Ca. P. pyri’.

This collaborative work by over 180 researchers from 40+ countries addresses the challenges posed by “phantom agents”—putative pathogenic agents named in literature without supporting data on their existence. Those agents remain on regulatory lists, creating barriers in trade and plant certification. Historically identified based solely on symptoms, these agents lack isolates or sequence data, making reliable detection or risk assessment impossible. After reviewing over 120 such agents across 10 key plant genera, we recommend their removal from regulatory lists and call for revised standards aligned with modern diagnostics. This effort seeks to streamline germplasm exchange, benefiting global agriculture by removing the constraints imposed by phantoms.

Pseudomonas syringae pv. syringae is the main causal agent of bacterial canker in sweet cherry in Chile, causing significant economic losses. Cultivars exhibit diverse susceptibility in the field and the molecular mechanisms underlying the differential responses remain unclear. RNA-seq analysis was performed to characterize the transcriptomic response in cultivars Santina and Bing (less and more susceptible to P. syringae pv. syringae, respectively) after 1 and 7 days post-inoculation (dpi) with the bacterium. Symptoms of bacterial canker became evident from the fifth day. At 1 dpi, cultivar Santina showed a faster response to infection and a larger number of differentially expressed genes (DEGs) than cultivar Bing. At 7 dpi, cultivar Bing almost doubled its DEGs, while cultivar Santina tended to the normal DEG levels. P. syringae pv. syringae infection downregulated the expressions of key genes of the photosynthesis process at 1 dpi in the less susceptible cultivar. The results suggest that the difference in susceptibility to P. syringae pv. syringae is linked to the timeliness of pathogen recognition, limiting the bacteria’s dispersion through modeling its cell wall, and regulation of genes encoding photosynthesis pathway. Through this study, it has been possible to progress the knowledge of relevant factors related to the susceptibility of the two studied cherry cultivars to P. syringae pv. syringae.

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.

In Chile, edible herbs are mainly grown by small farmers. This type of horticultural crop typically requires intensive management because it is highly susceptible to insects, some of which transmit viruses that severely affect crop yield and quality. In 2019, in coriander plants tested negative for all previously reported viruses, RNA-Seq analysis of one symptomatic plant revealed a plethora of viruses, including one virus known to infect coriander, five viruses never reported in coriander, and a new cytorhabdovirus with a 14,180 nucleotide RNA genome for which the species name Cytorhabdovirus coriandrum was proposed. Since all the detected viruses were aphid-borne, aphids and weeds commonly growing around the coriander field were screened for viruses. The results showed the occurrence of the same seven viruses and the alfalfa mosaic virus, another aphid-borne virus, in aphids and weeds. Together, our findings document the presence of multiple viruses in coriander and the potential role of weeds as virus reservoirs for aphid acquisition.

One of the causal agents of bacterial canker is Pseudomonas amygdali pv. morsprunorum—Pam (formerly Pseudomonas syringae pv. morsprunorum). Recently detected in Chile, Pam is known to cause lesions in the aerial parts of the plant, followed by more severe symptoms such as cankers and gummosis in the later stages of the disease. This study presents the design of PCR and LAMP detection methods for the specific and sensitive identification of Pseudomonas amygdali pv. morsprunorum (Pam) from cherry trees. Twelve Pseudomonas isolates were collected, sequenced, and later characterized by Multi-locus Sequence Analysis (MLSA) and Average Nucleotide Identity by blast (ANIb). Three of them (11116B2, S1 Pam, and S2 Pam) were identified as Pseudomonas amygdali pv. morsprunorum and were used to find specific genes through RAST server, by comparing their genome with that of other Pseudomonas, including isolates from other Pam strains. The effector gene HopAU1 was selected for the design of primers to be used for both techniques, evaluating sensitivity and specificity, and the ability to detect Pam directly from plant tissues. While the PCR detection limit was 100 pg of purified bacterial DNA per reaction, the LAMP assays were able to detect up to 1 fg of purified DNA per reaction. Similar results were observed using plant tissues, LAMP being more sensitive than PCR, including when using DNA extracted from infected plant tissues. Both detection methods were tested in the presence of 30 other bacterial genera, with LAMP being more sensitive than PCR.

Bacterial canker caused by Pseudomonas syringae pv. syringae (Pss) is responsible for substantial loss to the production of sweet cherry in Chile. To date, the molecular mechanisms of the Pss–sweet cherry interaction and the disease-related genes in the plant are poorly understood. In order to gain insight into these aspects, a transcriptomic analysis of the sweet cherry cultivar ‘Lapins’ for differentially expressed genes (DEGs) in response to Pss inoculation was conducted. Three Pss strains, A1M3, A1M197, and 11116_b1, were inoculated in young twigs, and RNA was extracted from tissue samples at the inoculation site and distal sections. RNA sequencing and transcriptomic expression analysis revealed that the three strains induced different patterns of responses in local and distal tissues. In the local tissues, A1M3 triggered a much more extensive response than the other two strains, enriching DEGs especially involved in photosynthesis. In the distal tissues, the three strains triggered a comparable extent of responses, among which 11116_b1 induced a group of DEGs involved in defense responses. Furthermore, tissues from various inoculations exhibited an enrichment of DEGs related to carbohydrate metabolism, terpene metabolism, and cell wall biogenesis. This study opened doors to future research on the Pss–sweet cherry interaction, immunity responses, and disease control.

Detection and classification of phytoplasmas mainly rely on amplification of the 16S rRNA gene followed by RFLP analysis and/or sequencing, because these organisms lack complete phenotypic characterization. Other conserved genomic loci have been exploited as additional molecular markers for phytoplasma differentiation. Two loci, SSU12p and LSU36p, selected by whole-genome comparison of 12 phytoplasma strains, were used for primer design, and were successfully tested on DNA samples from plants infected by phytoplasmas belonging to ten 16S ribosomal groups. The phylogenetic trees inferred from SSU12p and LSU36p loci were highly congruent to the trees derived from 16S rRNA and tuf genes of the same phytoplasma strains. Virtual RFLP analysis of the amplified SSU12p gene showed distinct patterns for most of the phytoplasma ribosomal subgroups tested. These results show that SSU12p and LSU36p genes are reliable additional markers for phytoplasma detection and differentiation.