Ontology highlight
ABSTRACT:
PROVIDER: PRJNA661345 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12586309.fastq.gz | Fastqsanger.gz | |||
| SRR12586310.fastq.gz | Fastqsanger.gz | |||
| SRR12586311.fastq.gz | Fastqsanger.gz | |||
| SRR12586312.fastq.gz | Fastqsanger.gz | |||
| SRR12586313.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: This study was to explore the underlying molecular mechanism of temperature effects on fruit quality during shelf life. The transcriptome data of peach fruits stored in high temperature (HT, 35 °C) and common temperature (CT, 25 °C) conditions were measured and compared. Methods: Red flesh peach (Prunus persica L. Batsch cv. Tianxianhong) fruits with consistent color, shape and weight were selected and kept at 5 °C for 2 days after the day of harvest. Then, these fruits were randomly divided into two groups. One group was stored at CT for 7 days, and the other was stored at HT for 7 days. During storage, fruits were sampled at day 1, 2 and 3 as early stage as well as day 5, 6 and 7 as later stage. Total RNA of each sample was extracted and used to construct 24 RNA libraries. RNA sequencing was performed on an Illumina HiSeq 2500 platform. The differences in transcriptome, ethylene production, pulp softening of postharvest peach fruits were compared between CT and HT storage conditions Results: Our results showed that HT conditioning after 5 °C is better than CT to maintaining fruit quality during shelf life due to MEKK1-MKK2-MPK4/6 signal transduction and low level of ethylene and auxin biosynthesis enzymes which may affect genes related to softening and membrane stability through ethylene response factors (ERFs) and auxin response factors (ARFs).
2020-06-27 | GSE122868 | GEO
Project description:Fleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCODE data of 355 transcriptome, 66 accessible chromatin, 160 histone and 45 DNA methylation profiles from eleven fleshy fruit species revealed three types of transcriptional feedback loops controlling ripening. Eudicots peach, papaya and melon evolved their circuits using carpel senescence NAC genes, whereas tomato, apple and pear utilized floral identity MADS genes derived from recent whole-genome-duplications. The monocot banana used both, forming a unique dual-loop circuit. Genes in these circuits and their tissue-specific H3K27me3 mark could be traced back to both dry fruits and ethylene-independent fleshy fruits, suggesting that the ethylene-dependent ripening mechanisms evolved from pre-existing genetic and epigenetic pathways in the ancestral angiosperms. FruitENCODE provides a comprehensive annotation of functional elements for fleshy fruit crops and new insight into the origins of climacteric fruit ripening.
2018-07-04 | GSE116581 | GEO
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:Gene expression in feeding larvae reciprocally transplanted into snowberry and apple fruits
2015-10-01 | GSE66975 | GEO
Project description:Bull’s eye rot is one of the most severe diseases that may affect apples during storage. It is caused by the fungus Neofabraea vagabunda, and the mechanism by which the pathogen infects the fruits is only partially understood. In particular, very little is known about the molecular mechanisms regulating the interaction between the pathogen and the host during symptoms development. Despite different apple cultivars show different levels of resistance to the pathogen, the genetic basis of these responses are unknown. In order to understand the molecular mechanisms occurring in the apple fruit during N. vagabunda infection, a large-scale transcriptome study by RNA-Seq analysis was performed, comparing fruits of the sensitive ‘Roho’ cultivar and the resistant cultivar ‘Ariane’ after artificial infection with N. vagabunda and a storage period of 4 months.
2024-03-06 | E-MTAB-13465 | biostudies-arrayexpress
Project description:Background Field observations and a few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited. Results The isolation of 455 genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach (Prunus persica, cv Fantasia) seed and mesocarp throughout development by means of µPEACH 1.0, the first peach microarray. Genes differentially expressed in the two organs and specific of developmental stages had been identified, and some were validated as markers. Genes representative of the main functional categories are present, among which several transcription factors such as MADS-box, bZIP, Aux/IAA, AP2, WRKY, and HD. Some of these showed a similar transcription profile in the two organs, while others displayed an opposite pattern, being more expressed in embryo at early development and in mesocarp at ripening. Conclusions The µPEACH1.0, although developed from ripe fruit ESTs, resulted in being suitable for studying seed/mesocarp interactions. Among the differentially expressed genes, marker genes specific for organ and stage of development have been selected. Comparisons were carried out by pooling stage 1 and 2 (named early development, e) and stage 3 and 4 (named late development, l), separately for mesocarp (M) and seed (S) of cultivar Fantasia, and using a simple loop experimental design. RNA has been extracted from fruit harvest at above-mentioned stages of development. At least four hybridizations have been conducted for a total of four technical replicates (with dye-swap).
2011-06-27 | E-GEOD-22582 | biostudies-arrayexpress
Project description:The self-abscising characteristic of fruit is a prominent trait for labor-saving cultivation in apple (Malus × domestica). Up to 30 days after full bloom, early abscission leaves only central fruit in a cluster, while four lateral fruits are abscised. Since fruit abscission is possibly induced during earlier phases of fruit development, samples were collected at full bloom and 10 days after full bloom. Comparative analysis between central and lateral pedicels in self-abscising apple can be used to identify the genes that trigger the abscission mechanism, as the destinies of the pedicels in a cluster are obvious. Transcriptome analysis was performed using RNA-Seq to compare expression profiles between the surviving central pedicel to be survived and abscised lateral pedicel to be abscised from self-abscising apple. A total of 797,647 ESTs were assembled into 65,876 contigs which were annotated and analyzed with using Blast2GO. A total of 1,585 differentially expressed genes in central and lateral pedicels were identified using the NOISeq software. , and these genes were were characterized using the MapMan ontology software. Transcription factors involved in vascular bundle differentiation functioned in the central pedicel, while the signaling cascade of IAA14/SLR-ARF7, which progressed during lateral root emergence from primary roots, operated in lateral pedicels. Future studies should explore associations between the mechanisms of lateral root emergence and pedicel abscission during early phases of fruit development, as well as the interconnection among hormones.
2017-08-05 | GSE60091 | GEO
Project description:Background Field observations and a few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited. Results The isolation of 455 genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach (Prunus persica, cv Fantasia) seed and mesocarp throughout development by means of µPEACH 1.0, the first peach microarray. Genes differentially expressed in the two organs and specific of developmental stages had been identified, and some were validated as markers. Genes representative of the main functional categories are present, among which several transcription factors such as MADS-box, bZIP, Aux/IAA, AP2, WRKY, and HD. Some of these showed a similar transcription profile in the two organs, while others displayed an opposite pattern, being more expressed in embryo at early development and in mesocarp at ripening. Conclusions The µPEACH1.0, although developed from ripe fruit ESTs, resulted in being suitable for studying seed/mesocarp interactions. Among the differentially expressed genes, marker genes specific for organ and stage of development have been selected.
2011-06-27 | GSE22582 | GEO