Potato Virus Y Infection Alters Small RNA Metabolism and Immune Response in Tomato.

Potato virus Y (PVY) isolate PVYC-to induces growth reduction and foliar symptoms in tomato, but new vegetation displays symptom recovery at a later stage. In order to investigate the role of micro(mi)RNA and secondary small(s)RNA-regulated mechanisms in tomato defenses against PVY, we performed sRNA sequencing from healthy and PVYC-to infected tomato plants at 21 and 30 days post-inoculation (dpi). A total of 792 miRNA sequences were obtained, among which were 123 canonical miRNA sequences, many isomiR variants, and 30 novel miRNAs. MiRNAs were mostly overexpressed in infected vs. healthy plants, whereas only a few miRNAs were underexpressed. Increased accumulation of isomiRs was correlated with viral infection. Among miRNA targets, enriched functional categories included resistance (R) gene families, transcription and hormone factors, and RNA silencing genes. Several 22-nt miRNAs were shown to target R genes and trigger the production of 21-nt phased sRNAs (phasiRNAs). Next, 500 phasiRNA-generating loci were identified, and were shown to be mostly active in PVY-infected tissues and at 21 dpi. These data demonstrate that sRNA-regulated host responses, encompassing miRNA alteration, diversification within miRNA families, and phasiRNA accumulation, regulate R and disease-responsive genes. The dynamic regulation of miRNAs and secondary sRNAs over time suggests a functional role of sRNA-mediated defenses in the recovery phenotype.

Ozone treatments activate defence responses against Meloidogyne incognita and Tomato spotted wilt virus in tomato.

BACKGROUND: Ozonated water (O3 wat) soil drench and/or foliar spray applications were evaluated for their potential to control the root-knot nematode Meloidogyne incognita (RKN) and the airborne pathogen Tomato spotted wilt virus (TSWV) in tomato. We investigated how O3 wat modulates the salicylic acid/jasmonic acid/ethylene (SA/JA/ET) signalling network in the host, locally and systemically, to induce resistance to nematode and virus. RESULTS: The application as soil drench was effective in reducing the number of galls and egg masses, but did not reduce the incidence and severity of TSWV infection. Conversely, O3 wat applied by foliar spray decreased TSWV disease incidence and severity (-20%), but was not able to control M. incognita infection. SA-related genes were generally upregulated in both locally treated and systemically reached tissues, showing a positive action of the O3 wat treatment on SA signalling. Neither O3 wat application method significantly altered JA-related gene expression in either direction. ET-related genes were differentially regulated by root or leaf treatments, indicating that O3 wat may have different effects on ET-mediated signalling in different organs. JA/ET/SA related pathways were differentially modulated by O3 wat in the presence of either RKN or TSWV. CONCLUSION: O3 wat had a higher efficacy when applied directly to organs challenged by the pathogens, although it was potentially able to stimulate defence responses through the activation of SA signalling. Owing to its safety and effectiveness in controlling nematode and virus infections, O3 wat can be considered as a possible alternative tool for sustainable disease management practices. © 2019 Society of Chemical Industry.

Metabarcoding Analysis of Phytophthora Diversity Using Genus-Specific Primers and 454 Pyrosequencing.

A metabarcoding method based on genus-specific primers and 454 pyrosequencing was utilized to investigate the genetic diversity of Phytophthora spp. in soil and root samples of potted plants, from eight nurseries. Pyrosequencing enabled the detection of 25 Phytophthora phylotypes distributed in seven different clades and provided a much higher resolution than a corresponding cloning/Sanger sequencing approach. Eleven of these phylotypes, including P. cactorum, P. citricola s.str., P. palmivora, P. palmivora-like, P. megasperma or P. gonapodyides, P. ramorum, and five putative new Phytophthora species phylogenetically related to clades 1, 2, 4, 6, and 7 were detected only with the 454 pyrosequencing approach. We also found an additional 18 novel records of a phylotype in a particular nursery that were not detected with cloning/Sanger sequencing. Several aspects confirmed the reliability of the method: (i) many identical sequence types were identified independently in different nurseries, (ii) most sequence types identified with 454 pyrosequencing were identical to those from the cloning/Sanger sequencing approach and/or perfectly matched GenBank deposited sequences, and (iii) the divergence noted between sequence types of putative new Phytophthora species and all other detected sequences was sufficient to rule out sequencing errors. The proposed method represents a powerful tool to study Phytophthora diversity providing that particular attention is paid to the analysis of 454 pyrosequencing raw read sequences and to the identification of sequence types.