Prunus armeniaca cultivar:Jiannali
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PROVIDER: PRJNA506310 | ENA |
REPOSITORIES: ENA
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Project description:BackgroundA complete and hardened endocarp is a typical trait of drupe fruits. However, the 'Liehe' (LE) apricot cultivar has a thin, soft, cleavable endocarp that represents 60.39% and 63.76% of the thickness and lignin content, respectively, of the 'Jinxihong' (JG) apricot (with normal hardened-endocarp). To understand the molecular mechanisms behind the LE apricot phenotype, comparative transcriptomes of Prunus armeniaca L. were sequenced using Illumina HiSeq™ 2500.ResultsIn this study, we identified 63,170 unigenes including 15,469 genes >1000 bp and 25,356 genes with Gene Function annotation. Pathway enrichment and expression patterns were used to characterize differentially expression genes. The DEGs encoding key enzymes involved in phenylpropanoid biosynthesis were significantly down-regulated in LE apricot. For example, CAD gene expression levels, encoding cinnamyl alcohol dehydrogenase, were only 1.3%, 0.7%, 0.2% and 2.7% in LE apricot compared with JG cultivar at 15, 21, 30, 49 days after full bloom (DAFB). Furthermore, transcription factors regulating secondary wall and lignin biosynthesis were identified. Especially for SECONDARY WALL THICKENING PROMOTING FACTOR 1 (NST 1), its expression levels in LE apricot were merely 2.8% and 9.3% compared with JG cultivar at 15 and 21 DAFB, respectively.ConclusionsOur comparative transcriptome analysis was used to understand the molecular mechanisms underlie the endocarp-cleaving phenotype in LE apricot. This new apricot genomic resource and the candidate genes provide a useful reference for further investigating the lignification during development of apricot endocarp. Transcription factors such as NST1 may regulate genes involved in phenylpropanoid pathway and affect development and lignification of the endocarp.
| S-EPMC5387262 | biostudies-literature
Project description:Prunus armeniaca Transcriptome or Gene expression
| PRJNA590556 | ENA
Project description:Prunus armeniaca Transcriptome or Gene expression
| PRJNA774923 | ENA
Project description:Prunus armeniaca L.cultivar LunTaiBaiXing (Fruit) Transcriptome or Gene expression
| PRJNA369228 | ENA
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: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
Project description:In this work, an electrochemical oscillation system has been developed using the Belousov–Zhabotinsky reaction. The effect of the combination of each reagent, reaction temperature, and stirring speed on the induction period, oscillating period, and oscillating life were optimized. The nuts of Prunus persica, Prunus davidiana, and Prunus armeniaca have been widely used for medical purposes. The proposed electrochemical oscillation system was then used for the identification of P. persica, P. davidiana, and P. armeniaca. Three nuts exhibited very different electrochemical oscillation profiles. The dendrogram was divided into three main principal infrageneric clades. Each cluster only contains one species, suggesting that no outlier was observed in this study. Based on the discussed results, we proposed a simple method for herbal medicine identification.
| S-EPMC7516034 | biostudies-literature