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Involvement of different plant viruses in the activation of RNA silencing-related genes and the defensive response against Plum pox virus of ‘GF305’ peach (Prunus persica) grafted with ‘Garrigues’ almond (P. dulcis)

ABSTRACT: Involvement of different plant viruses in the activation of RNA silencing-related genes and the defensive response against Plum pox virus of ‘GF305’ peach (Prunus persica) grafted with ‘Garrigues’ almond (P. dulcis)

PROVIDER: PRJNA780811 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16955447.fastq.gz	Fastqsanger.gz
	SRR16955448.fastq.gz	Fastqsanger.gz
	SRR16955449.fastq.gz	Fastqsanger.gz
	SRR16955450.fastq.gz	Fastqsanger.gz
	SRR16955451.fastq.gz	Fastqsanger.gz

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Involvement of different plant viruses in the activation of RNA silencing-related genes and the defensive response against Plum pox virus of ‘GF305’ peach (Prunus persica) grafted with ‘Garrigues’ almond (P. dulcis)

Project description:Plum pox virus (PPV) causes the serious sharka disease in Prunus trees. Peach [P. persica (L.) Batsch] trees are severely affected by PPV and no definitive source of genetic resistance has been identified at this moment. Previous results showed, however, that PPV-resistant ‘Garrigues’ almond [P. dulcis (Mill.) D.A. Webb] was able to transfer its resistance to ‘GF305’ peach through grafting, preventing these trees from PPV infection and reducing symptomatology and viral load in PPV-infected plants. A recent study tried to identify genes responsible for this effect by studying mRNA expression through RNAseq data in peach and almond plants, before and after grafting, and before and after PPV infection. In this work, we used the same peach and almond samples, but focused the high-throughput analyses on small RNAs (sRNAs) expression. We studied massive sequencing data and found an interesting pattern of sRNAs overexpression linked to antiviral defense genes that suggested activation of these genes followed by downregulation to basal levels. We also discovered that ‘Garrigues’ almond plants were infected by different plant viruses that were transferred to peach plants. The large amounts of viral sRNAs found in grafted peaches indicated a strong RNA silencing antiviral response and led us to postulate that these plant viruses could be collaborating by cross-protection in the observed ‘Garrigues’ effect.

2022-11-02 | GSE188935 | GEO

Plum pox virus

Project description:Plum pox virus Genome sequencing and assembly

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Absence of major epigenetic and transcriptomic changes accompanying the interspecific cross between peach and almond

Project description:We analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in their F1 hybrid using high-throughput sequencing tecnhologies. We can conclude that the merging of the two parental genomes in the P. persica x P. dulcis hybrid does not result in a “genomic shock” with significant changes in the DNA methylation or in the transcription.

2022-08-10 | GSE198152 | GEO

Gene Expression Analysis of Induced Plum pox virus (Sharka) Resistance in Peach (Prunus persica) by Almond (P. dulcis) Grafting.

Project description:No natural sources of resistance to Plum pox virus (PPV, sharka disease) have been identified in peach. However, previous studies have demonstrated that grafting a "Garrigues" almond scion onto "GF305" peach rootstock seedlings heavily infected with PPV can progressively reduce disease symptoms and virus accumulation. Furthermore, grafting a "Garrigues" scion onto the "GF305" rootstock has been shown to completely prevent virus infection. This study aims to analyse the rewiring of gene expression associated with this resistance to PPV transmitted by grafting through the phloem using RNA-Seq and RT-qPCR analysis. A total of 18 candidate genes were differentially expressed after grafting "Garrigues" almond onto healthy "GF305" peach. Among the up-regulated genes, a HEN1 homolog stands out, which, together with the differential expression of RDR- and DCL2-homologs, suggests that the RNA silencing machinery is activated by PPV infection and can contribute to the resistance induced by "Garrigues" almond. Glucan endo-1,3-beta D-glucosidase could be also relevant for the "Garrigues"-induced response, since its expression is much higher in "Garrigues" than in "GF305". We also discuss the potential relevance of the following in PPV infection and "Garrigues"-induced resistance: several pathogenesis-related proteins; no apical meristem proteins; the transcription initiation factor, TFIIB; the speckle-type POZ protein; in addition to a number of proteins involved in phytohormone signalling.

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Almond x Peach interspecific hybrid

Project description:Identification of putative markers of noninfectious bud failure in almond (Prunus dulcis [Mill] D.A. Webb) through genome wide DNA methylation profiling and gene expression analysis in an almond x peach hybrid population

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Phytohormone Signaling of the Resistance to Plum pox virus (PPV, Sharka Disease) Induced by Almond (Prunus dulcis (Miller) Webb) Grafting to Peach (P. persica L. Batsch).

Project description:Plum pox virus (PPV, sharka) is a limiting factor for peach production, and no natural sources of resistance have been described. Recent studies, however, have demonstrated that grafting the almond cultivar "Garrigues" onto the "GF305" peach infected with Dideron-type (PPV-D) isolates progressively reduces disease symptoms and virus accumulation. Furthermore, grafting "Garrigues" onto "GF305" prior to PPV-D inoculation has been found to completely prevent virus infection, showing that resistance is constitutive and not induced by the virus. To unravel the phytohormone signaling of this mechanism, we analyzed the following phytohormones belonging to the principal hormone classes: the growth-related phytohormones cytokinin trans-zeatin (tZ) and the gibberellins GA? and GA?; and the stress-related phytohormones ethylene acid precursor 1-aminocyclopropane-1-carboxylic acid (ACC), abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA). PPV inoculation produced a significant increase in GA? and ABA in peach, and these imbalances were related to the presence of chlorosis symptoms. However, grafting "Garrigues" almond onto the PPV-inoculated "GF305" peach produced the opposite effect, reducing GA? and ABA contents in parallel to the elimination of symptoms. Our results showed the significant implication of SA in this induced resistance in peach with an additional effect on tZ and JA concentrations. This SA-induced resistance based in the decrease in symptoms seems to be different from Systemic Acquired Resistance (SAR) and Induced Systemic Resistance (ISR), which are based in other reactions producing necrosis. Further studies are necessary, however, to validate these results against PPV-D isolates in the more aggressive Marcus-type (PPV-M) isolates.

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Transcriptome analysis of compatible and incompatible pollen-pistil interactions in almond (Prunus dulcis)

Project description:The cultivated almond exhibits self-incompatibility of the gametophytic type regulated by the S-locus, and expressed in pistil (S-RNase) and in pollen (SFB protein). The aim of this study is to clarify the transcription pattern of these 2 S-genes and to identify additional components of the gametophytic self-incompatibility system in almond. With this aim, A2-198 (self compatible) and ITAP-1 (self incompatible) almond selections were used: RNA-seq of pistils of these two accessions both un-pollinated and pollinated with A2-198 pollen were carried out.

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Project description:Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence.

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Transcription profiling of Arabidopsis leaf tissues and protoplasts in response to Plum pox virus infection

Project description:Virus infection induces activation and suppression of global gene expression in the host. Profiling gene expression changes in the host may provide insights into the molecular mechanisms that underlie host physiological and phenotypic responses to virus infection. In this study, the Arabidopsis Affymetrix ATH1 whole genome array was used to assess global gene expression changes in Arabidopsis thaliana plants infected with Plum pox virus (PPV). To identify early genes in response to PPV infection, an Arabidopsis synchronized single-cell transformation system was developed. Arabidopsis protoplasts were transfected with a PPV infectious clone, PPV-SK68 and global gene expression changes in the transfected protoplasts were profiled. Experiment Overall Design: For PPV infection in Arabdiopsis leaves, eight independent hybridizations were performed using total RNA isolated from three independent biological replicates of the virus-infected or mock-inoculated control samples. Experiment Overall Design: For PPV infection in Arabidopsis protoplasts, 24 gene chips in total were used to hybridize with RNA isolated from protoplasts transfected with PPV infectious clone and PPV deletion mutant.

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