Ontology highlight
ABSTRACT:
PROVIDER: PRJNA822360 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18583984_1.fastq.gz | Fastqsanger.gz | |||
| SRR18583984_2.fastq.gz | Fastqsanger.gz | |||
| SRR18583985_1.fastq.gz | Fastqsanger.gz | |||
| SRR18583985_2.fastq.gz | Fastqsanger.gz | |||
| SRR18583986_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
Similar Datasets
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
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
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
Project description:Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The Prunus persica (peach) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Until now, little was known about the function of WEEP protein despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size-exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide new insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.
2023-12-13 | GSE250141 | GEO
Project description:To determine how dormancy breaking agent, hydrogen cyanamide (HC) advances bud break in peach (Prunus persica), this research compared the transcriptome of buds of low-chill ‘TropicBeauty’ peach trees treated with 1% (v/v) HC and that of non-treated trees at 3 and 7 days after treatment (DAT), respectively, using RNA sequencing analysis. The peak of total bud break occurred 6 weeks earlier in the HC treated trees (at 32 DAT) than the non-treated trees (at 74 DAT). There were 1312 and 1095 differentially expressed genes (DEGs) at 3 and 7 DAT, respectively. At 3 DAT, DEGs related to oxidative stress, including response to hypoxia, lipid oxidation, and reactive oxygen species (ROS) metabolic process, were up regulated in HC-treated buds. Additionally, DEGs encoding enzymes for ROS scavenging and pentose phosphate pathway were up regulated at 3 DAT but were not differently expressed at 7 DAT, indicating a temporary demand for defense mechanisms against HC-triggered oxidative stress. Up regulation of DEGs for cell division and development at 7 DAT, which were down regulated at 3 DAT, suggests cell activity was initially suppressed but enhanced within 7 days following the treatment. At 7 DAT, DEGs related to cell wall degradation and modification were up-regulated, possibly responsible for the burst of buds. The results of this study strongly suggest that HC induces transient oxidative stress shortly after application leading to the release of bud dormancy and, subsequently, causes an increase in cell activity and cell wall loosening, thereby accelerating bud break in peach.
2020-03-12 | GSE128158 | GEO
Project description:MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development. To identify more conserved and peach-speciM-oM-,M-^Ac miRNAs and their target genes and to understand further the mechanism of miRNA-regulated target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three different tissues for deep sequencing.
2014-01-01 | E-GEOD-49579 | biostudies-arrayexpress
Project description:MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development.
2014-01-01 | GSE49579 | GEO
Project description:Prunus persica x Prunus persica var. nucipersica Map
| PRJNA156965 | ENA
Project description:Prunus persica x Prunus persica var. nucipersica Map
| PRJNA156969 | ENA
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