Ontology highlight
ABSTRACT:
PROVIDER: PRJNA587386 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10390615_1.fastq.gz | Fastqsanger.gz | |||
| SRR10390615_2.fastq.gz | Fastqsanger.gz | |||
| SRR10390616_1.fastq.gz | Fastqsanger.gz | |||
| SRR10390616_2.fastq.gz | Fastqsanger.gz | |||
| SRR10390617_1.fastq.gz | Fastqsanger.gz |
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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:Tea (Camellia sinensis (L.) O. Kuntze) is an important non-alcoholic commercial beverage crop. Tea tree is a perennial plant, and winter dormancy is its part of biological adaptation to environmental changes. We recently discovered a novel tea tree cultivar that can generate tender shoots in winter, but the regulatory mechanism of this ever-growing tender shoot development in winter is not clear. In this study, we conducted a proteomic analysis for identification of key genes and proteins differentially expressed between the winter and spring tender shoots, to explore the putative regulatory mechanisms and physiological basis of its ever-growing character during winter.
2022-02-23 | PXD008958 | Pride
Project description:A transcriptome analysis was applied on two peach (Prunus persica L.) cultivars with different sensitivity to low temperature regimes to identify cold-responsive genes that might be involved in tolerance to long low temperature storage. Peach fruit from ‘Morettini No2’ and ‘Royal Glory’, a sensitive and a tolerant, to chilling injury cultivars, respectively, were harvested at commercial maturity stage and allowed to ripen at room temperature (25°C) or subjected to 4 and 6-weeks of cold storage (0°C, 95% R.H.) followed by ripening at room temperature. Microarray experiments, employing the peach microarray platform (μ PEACH 1.0), were carried out by comparing harvested fruit against 4- and 6-week cold-stored fruit. The analysis identified 173 and 313 genes that were differentially expressed in ‘Morettini No2’ and ‘Royal Glory’ fruit after 4 weeks, respectively. However, the 6 weeks cold storage provoked a decrease in the total number of genes differentially expressed in both cultivars. RNA blot analysis validated the differential expression of certain genes showed in microarray data. Among these genes, two heat shock proteins (hsps), a putative β-D-xylosidase, an expansin, a dehydrin and a pathogenesis-related protein PR-4B precursor were induced during cold storage in both cultivars. The induction of hsps and the putative β-D-xylosidase appeared to be independent on the duration of postharvest treatment. On the other hand, transcript levels of lipoxygenase were quite constant during postharvest ripening, while a strong reduction or disappearance was observed after cold storage. A dehydration-induced RD22-like protein showed a reduction in the accumulation of transcripts during postharvest ripening independently on the temperature conditions. Overall, the current study shed some light on the molecular aspects of cold stress in peach fruit quality and identified some ripening and/or cold-induced genes which function need further elucidation.
2011-08-26 | GSE18280 | GEO
Project description:Cold storage (CS) is widely used to extend fruit postharvest. In peach, chilling injuries may cause intense juice loss leading to a dry âwoollyâ texture of the fruit flesh. The disturbance, named woolliness, is associated to abnormal pectin metabolism and results in anatomical and physiological alterations. Application of gibberellic acid (GA) at the initial stages of pit hardening has been shown to impair woolliness incidence, however the mechanisms controlling the response remain unknown. We have employed genome wide transcription analyses to investigate the effects of GA application and CS of peaches. Approximately half (48.26%, 13846) of the investigated genes exhibited significant differential expression in response to the treatments. Gene ontology classes associated to cellular and developmental processes were overrepresented among the differentially regulated genes, whereas sequences classified in cell death and immune response categories were underrepresented. Gene set enrichment analyses demonstrated a predominant role of CS in repressing the transcription of genes associated to cell wall metabolism. In contrast, genes involved in hormone metabolism and signaling exhibited a more complex transcriptional response to the factors, indicating an extensive network of crosstalk between GA and low temperatures. Time course transcriptional profiling analyses also confirmed the involvement of cell wall metabolism genes in woolliness onset in peach. Overall, our results provide further insights on the mechanisms controlling the complex phenotypes associated to postharvest textural changes in peach. Four samples (CONT, CONTcs, GA3, GA3cs), each with three biological replicates (R1, R2 and R3), were analyzed. Control samples (CONT and CONTcs) consist of peach mesocarp not treated with GA3 at pit hardening, and either assayed at harvest (CONT) or after 15 days of cold storage (CONTcs). GA3 samples (GA3 and GA3cs) consist of peach mesocarp treated with GA3 at pit hardening, and either assayed at harvest (GA3) or after 15 days of cold storage (GA3cs).
2015-10-29 | E-GEOD-71460 | biostudies-arrayexpress
Project description:Proteomics analyses of roots and shoots of O. sativa plants exposed to cold stress.
2022-02-16 | PXD028712 | Pride
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2014-10-15 | GSE57895 | 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:The fruit of melting-flesh peach cultivars produce high levels of ethylene caused by high expression of PpACS1, resulting in rapid fruit softening at the late-ripening stage. In contrast, the fruit of stony hard peach cultivars do not soften and produce little ethylene due to low expression of PpACS1. To elucidate the mechanism for suppressing PpACS1 expression in stony hard peaches, a microarray analysis was performed. Several genes that displayed similar expression patterns as PpACS1 were identified and shown to be IAA-inducible genes. Change in gene expression according to growth of fruits in 'melting peach M-bM-^@M-^XAkatsukiM-bM-^@M-^Y fruit sampled at 92, 98, 104 and 106 day after full bloom (DAB). Propylene induced gene expression stony peach M-bM-^@M-^XManamiM-bM-^@M-^Y and M-bM-^@M-^XOdorokiM-bM-^@M-^Y harvested at commercial maturity (Tatsuki et al., 2006).
2013-03-27 | E-GEOD-45490 | biostudies-arrayexpress
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:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed
2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress