Ontology highlight
ABSTRACT:
PROVIDER: PRJNA810952 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18173439.fastq.gz | Fastqsanger.gz | |||
| SRR18173440.fastq.gz | Fastqsanger.gz | |||
| SRR18173441.fastq.gz | Fastqsanger.gz | |||
| SRR18173442.fastq.gz | Fastqsanger.gz | |||
| SRR18173443.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this study was to elucidate the potential use of microarray technology, developed in model species, in related, yet phenotypically distinct, species where few or no information are available. Considering the high degree of sequence conservation within the Rosaceae family and, in particular, among the Prunus species we employed the first available peach oligonucleotide microarray (µPEACH 1.0) for studying the transcrptomic profile during apricot fruit development (Prunus armeniaca L., cv. 'Goldrich'). Fruit material was harvested at three distinct stages, corresponding to immature-green stage (6 weeks before fully-ripe stage), mature-firm-ripe stage (change of peel color, 1 week before fully-ripe stage) and at fully-ripe stage and designated as S1, S2 and S3 stages, respectively. Apricot targets cDNA, when applied the µPEACH1.0, were showing significant hybridization with an average of 43% of spotted targets validating the use of μPEACH1.0 to profile the transcriptome of apricot fruit during development and ripening. Microarray analysis carried out on immature and ripe peach and apricot fruit separately pointed out that 70% of genes differentially expressed was detectable the same pattern of expression in both species. This result indicates that the transcriptome of immature and ripe fruit are quite similar in apricot and peach, but also highlighted the presence of transcript changes specie-specific. When μPEACH1.0 was used to profile apricot developing fruit were identified 400 and 74 genes differetially expressed during the transition from S1 to S2 stage and from S2 to S3 stage, respectively. Intriguingly, a considerable number of auxin action regulators (AUX/IAA) and of genes coding heat shock proteins (hsp) were highly up-regulated at the onset and late of ripening phase, respectively.The comparison between the expression profiles of these apricot genes and their peach hortologues showed a similar pattern for AUX/IAA and quite different for hsps. This result suggests a similar role for AUX/IAA in both species and a more important involvement for hsps in the apricot fruit ripening.
2011-01-12 | GSE19828 | GEO
Project description:Bud dormancy is a critical developmental process for perennial plant survival, and also an important physiological phase that affects the next season’s growth of temperate fruit trees. Bud dormancy is regulated by multiple genetic factors, and affected by various environmental factors, tree age and vigor. To understand molecular mechanism of bud dormancy in Japanese apricot (Prunus mume Sieb. et Zucc.), we constructed a custom oligo DNA microarray covering the Japanese apricot dormant bud ESTs referring to peach (P. persica) genome sequence. Because endodormancy release is a chilling temperature-dependent physiological event, genes showing chilling-mediated differential expression patterns are candidates to control endodormancy release. Using the microarray constructed in this study, we monitored gene expression changes of dormant vegetative buds of Japanese apricot during prolonged artificial chilling exposure. In addition, we analyzed seasonal gene expression changes. ‘Nanko’ vegetative buds collected in November, and those exposed to chilling for 40 or 60 days were used as microarray samples. Among the 58539 different unigene probes, 2345 and 1059 genes were identified as being more than two-fold up-regulated and down-regulated, respectively, following chilling exposure for 60 days (P value < 0.05). The down-regulated genes included P. mume DORMANCY-ASSOCIATED MADS-box genes, which supported the previous quantitative RT-PCR and EST analyses showing that these genes are repressed by prolonged chilling treatments. The genes encoding lipoxygenase were remarkably up-regulated by prolonged chilling. Cluster analysis suggested that the expression of the genes showing expression changes by artificial chilling exposure were coordinately regulated by seasonal changes. Our parametric analysis of gene set enrichment suggested that genes related to jasmonic acid (JA) and oxylipin biosynthesis and metabolic processes were significantly up-regulated by prolonged chilling, whereas genes related to circadian rhythm were significantly down-regulated. The results obtained from the microarray analyses were verified by quantitative RT-PCR analysis of selected genes. Taken together, this study raised the possibility that the microarray platform constructed in this study is applicable for deeper understanding of molecular network related to agronomically important bud phisiologies including dormancy release.
2014-03-26 | GSE49368 | GEO
Project description:The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co-regulatory genes, are quite unknown. Therefore, to identify the genome-wide binding sites of PmTCP4 transcription factors and their co-regulatory genes, chromatin immunoprecipitation sequencing (ChIPSeq) was carried out. ChIP-Seq data produced the maximum enriched peaks in two Japanese apricot cultivars ‘Daqiandi’ (DQD) and ‘Longyan’ (LY), which showed that the majority ofDNA-protein interactions are relevant and have a significant function in binding sites. Moreover, 720 and 251 peak-associated genes regulated by PmTCP4 were identified in DQD and LY, respectively, and most of them were involved in the flower and pistil development process. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis and oxidative phosphorylation were the most enriched pathways in both cultivars and all identified genes related to these pathways were down-regulated. This study will provide a reference for a better understanding of the PmTCP4 regulatory mechanism during pistil abortion in Japanese apricot.
2020-09-06 | GSE132994 | GEO
Project description:Bud dormancy is a critical developmental process for perennial plant survival, and also an important physiological phase that affects the next seasonM-bM-^@M-^Ys growth of temperate fruit trees. Bud dormancy is regulated by multiple genetic factors, and affected by various environmental factors, tree age and vigor. To understand molecular mechanism of bud dormancy in Japanese apricot (Prunus mume Sieb. et Zucc.), we constructed a custom oligo DNA microarray covering the Japanese apricot dormant bud ESTs referring to peach (P. persica) genome sequence. Because endodormancy release is a chilling temperature-dependent physiological event, genes showing chilling-mediated differential expression patterns are candidates to control endodormancy release. Using the microarray constructed in this study, we monitored gene expression changes of dormant vegetative buds of Japanese apricot during prolonged artificial chilling exposure. In addition, we analyzed seasonal gene expression changes. M-bM-^@M-^XNankoM-bM-^@M-^Y vegetative buds collected in November, and those exposed to chilling for 40 or 60 days were used as microarray samples. Among the 58539 different unigene probes, 2345 and 1059 genes were identified as being more than two-fold up-regulated and down-regulated, respectively, following chilling exposure for 60 days (P value < 0.05). The down-regulated genes included P. mume DORMANCY-ASSOCIATED MADS-box genes, which supported the previous quantitative RT-PCR and EST analyses showing that these genes are repressed by prolonged chilling treatments. The genes encoding lipoxygenase were remarkably up-regulated by prolonged chilling. Cluster analysis suggested that the expression of the genes showing expression changes by artificial chilling exposure were coordinately regulated by seasonal changes. Our parametric analysis of gene set enrichment suggested that genes related to jasmonic acid (JA) and oxylipin biosynthesis and metabolic processes were significantly up-regulated by prolonged chilling, whereas genes related to circadian rhythm were significantly down-regulated. The results obtained from the microarray analyses were verified by quantitative RT-PCR analysis of selected genes. Taken together, this study raised the possibility that the microarray platform constructed in this study is applicable for deeper understanding of molecular network related to agronomically important bud phisiologies including dormancy release. In this study, we used chilling exposed bud samples (0, 40, 60 days starting at November) and seasonal monthly bud samples (June to March). For the samples in dataset 1 (three different time points during chilling treatment), three technical replicates (60K M-CM-^W 3 per sample) with three biological replicates were averaged, whereas three technical replicates were averaged for the samples in dataset 2 (10 different seasonal time points)
2014-03-26 | E-GEOD-49368 | biostudies-arrayexpress