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ABSTRACT: Gene expression analysis of induced Plum pox virus resistance in peach (Prunus persica) by almond (P. dulcis) grafting

PROVIDER: PRJNA712938 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13920627_1.fastq.gz	Fastqsanger.gz
	SRR13920627_2.fastq.gz	Fastqsanger.gz
	SRR13920628_1.fastq.gz	Fastqsanger.gz
	SRR13920628_2.fastq.gz	Fastqsanger.gz
	SRR13920629_1.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

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

Alteration of TAC1 expression in Prunus species leads to pleiotropic shoot phenotypes

Project description:Prunus persica (peach) trees carrying the ‘Pillar’ or ‘Broomy’ trait (br) have vertically oriented branches caused by loss of function mutations in a gene called TILLER ANGLE CONTROL 1 (TAC1). TAC1 encodes a protein in the IGT gene family that includes LAZY1 and DEEPER ROOTING 1 (DRO1), which regulat lateral branch and root orientations, respectively. Here, we found that some of the native TAC1 alleles in the hexaploid plum species Prunus domestica, which has a naturally more upright stature, contained a variable length trinucleotide repeat within the same exon 3 region previously found to be disrupted in pillar peach trees. RNAi silencing of TAC1 in plum resulted in trees with severely vertical branch orientations similar to those in pillar peaches but with an even narrower profile. In contrast, PpeTAC1 over-expression in plum led to trees with wider branch angles and more horizontal branch orientations. Pillar peach trees and transgenic plum lines exhibited pleiotropic phenotypes including differences in trunk and branch diameter, stem growth, and twisting branch phenotypes. Expression profiling of pillar peach trees revealed differential expression of numerous genes associated with biotic and abiotic stress, hormone responses, plastids, reactive oxygen, and secondary and cell wall metabolism. Collectively, the data provide important clues for understanding TAC1 function and show that alteration of TAC1 expression may have broad applicability to agricultural and ornamental tree industries.

2018-04-04 | GSE112649 | GEO

Common and strain-specific post-translational modifications of the potyvirus Plum pox virus coat protein in different hosts

Project description:Phosphorylation and O-GlcNAcylation are widespread post-translational modifications (PTMs) often sharing protein targets. Numerous studies have reported phosphorylation of plant virus proteins. In plants, research on O-GlcNAcylation lags behind regarding other eukaryotes and information about O-GlcNAcylated plant viral proteins is extremely scarce. The potyvirus Plum pox virus (PPV) causes sharka disease in Prunus trees, and also infects a wide range of experimental hosts. Capsid protein (CP) from virions of the PPV-R isolate purified from herbaceous plants can be extensively modified by O-GlcNAcylation and phosphorylation. In this study, a combination of proteomics and biochemical approaches has been employed to broaden knowledge of PPV CP PTMs. CP proved to be modified regardless it is assembled or not in mature particles. PTMs of CP occur in the natural host Prunus persica, similar to what happens in herbaceous plants. Additionally, we observe O-GlcNAcylation and phosphorylation are general features of different PPV strains, suggesting that roles of these modifications are part of overall strategies deployed during plant-virus interactions. Interestingly, phosphorylation at a casein kinase II motif conserved among potyviral CPs exhibits strain specificity in PPV; however, it does not display the critical role attributed to same modification in the CP of another potyvirus, Potato virus A.

2020-05-27 | PXD017780 | Pride

Project description:Plum pox virus populations in peach and American plum

| PRJNA881753 | ENA

Project description: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)

| PRJNA780811 | ENA

RNAseq for peach weeping and standard lateral shoot (branch) tips

Project description:Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325, having a 1.8-Kb deletion spanning the 5′ end. This gene, dubbed WEEP, was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity per- ception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications.

2018-03-21 | GSE112080 | GEO

Prunus dulcis x Prunus persica

Project description:Prunus dulcis x Prunus persica Map

| PRJNA164761 | ENA

Prunus persica x Prunus dulcis

Project description:Prunus persica x Prunus dulcis Map

| PRJNA80625 | ENA

Prunus dulcis x Prunus persica

Project description:Prunus dulcis x Prunus persica Map

| PRJNA164767 | ENA