A transcriptome study of a non-shedding fruit Elaeis oleifera palm
Ontology highlight
ABSTRACT:
ORGANISM(S): Elaeis oleifera
PROVIDER: GSE186050 | GEO | 2021/10/28
REPOSITORIES: GEO
Similar Datasets
Project description:To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.
2021-02-08 | GSE166314 | GEO
Project description:A transcriptome study of a non-shedding fruit Elaeis oleifera palm
| PRJNA773955 | ENA
Project description:In tomato, the mutants that lack the abscission zone (AZ) within pedicels are called a ‘jointless’ and are agronomically significant in that they increase the tomato fruit yield for industrial processing. We have employed DNA microarray expression analysis to identify genes with the potential to play a role in development of the pedicel abscission zone of tomato, and identified several classes of differentially regulated genes between pedicels of the AZ-forming line (wild-type) and pedicels of the non AZ-forming lines (jointless mutant and MC-suppressed transformant).
2010-07-03 | GSE22682 | GEO
Project description:In tomato, the mutants that lack the abscission zone (AZ) within pedicels are called a ‘jointless’ and are agronomically significant in that they increase the tomato fruit yield for industrial processing. We have employed DNA microarray expression analysis to identify genes with the potential to play a role in development of the pedicel abscission zone of tomato, and identified several classes of differentially regulated genes between pedicels of the AZ-forming line (wild-type) and pedicels of the non AZ-forming lines (jointless mutant and MC-suppressed transformant). Tomato flower pedicels were harvested at anthesis stage from the AZ-forming line (wild-type) and the non AZ-forming lines (jointless mutant and MC-suppressed transformant), and subjected to DNA microarray analyses. Experiments were performed twice with independently prepared samples.
2010-07-03 | E-GEOD-22682 | biostudies-arrayexpress
Project description:The aim of this study is to assess the global transcriptome changes during the shedding of the flower, which normally takes around 6 or 7 days. We selected four time points (from day 0 to day 6) and three different tissues within the flower bud; distal, abscission and proximal zones with three biological replicates. RNA extraction, library prep and paired end sequencing was performed. Our special interest is try to describe the changes in the abscission zone and the two adjacent tissues in order to get a whole picture of the shedding process. We performed a de novo assembly by Trinity and detected the transcripts and expression changes across spatial and temporal comparisons.
2017-12-31 | E-MTAB-6282 | biostudies-arrayexpress
Project description:Oil Palm Fruit Abscission Zone Transcriptome
| PRJNA700429 | ENA
Project description:We report the expression analysis of seed kernel in Camellia oleifera cultivars. In total 221 cultivars are sequenced by the Illumina sequencing experiments to obtain the gene expression profiles.
2021-12-12 | GSE190644 | GEO
Project description:Organ abscission is a general activity found in plants and its regulation is an important agronomical concern because the trait directly affects the harvesting efficiency of fruits or grains and the yields. Generally, abscission takes place at a specialized cell layer, which is called abscission zones (AZs). So far, investigations on organ abscission have been focused mainly on the cell activities during organ detachment. By contrast, little attention has been paid to the properties of AZ cells at the pre-abscission stage. The pre-abscission cells are at a turning point for initiating abscission; until an abscission initiating signal is provided, the AZ cells keep their physiological state, while once the signal occurs, the cells immediately change their state into the onset of abscission. In this study, to screen the genes involved in the regulation of abscission at the pre-abscission state, we investigated the gene expression profiles of tomato flower pedicels at anthesis. The screening revealed many genes that characterize cell identities in each pedicel region. We harvested tomato flower pedicels at the anthesis stage and divided them into three parts: the abscission zone (AZ) and the flanking proximal- (Prox) and distal- (Dis) regions. RNA was isolated and subjected to DNA microarray analyses. Experiments were performed three times with independently prepared samples.
2012-07-19 | E-GEOD-39519 | biostudies-arrayexpress
Project description:Organ abscission is a general activity found in plants and its regulation is an important agronomical concern because the trait directly affects the harvesting efficiency of fruits or grains and the yields. Generally, abscission takes place at a specialized cell layer, which is called abscission zones (AZs). So far, investigations on organ abscission have been focused mainly on the cell activities during organ detachment. By contrast, little attention has been paid to the properties of AZ cells at the pre-abscission stage. The pre-abscission cells are at a turning point for initiating abscission; until an abscission initiating signal is provided, the AZ cells keep their physiological state, while once the signal occurs, the cells immediately change their state into the onset of abscission. In this study, to screen the genes involved in the regulation of abscission at the pre-abscission state, we investigated the gene expression profiles of tomato flower pedicels at anthesis. The screening revealed many genes that characterize cell identities in each pedicel region.
2012-07-20 | GSE39519 | GEO
Project description:MicroRNAs (miRNAs) are endogenous, noncoding, smallRNAs that regulate gene expression at the post-transcriptional level during plant development, growth and seed germination. Among all medicinal plants, Moringa oleifera is one of the most useful trees for which, despite its diffusion, no information about its miRNAs and their respective target genes is available. In this research, we report results obtained from a high-throughput sequencing analysis performed with the Illumina platform. A total of 31,290,964 raw reads were produced from M. oleifera seed smallRNA library. First, we found 99 conserved miRNAs and 43 novel ones that we partially validated by qRT- PCR. Second, by comparing their expression abundances with those of other common plants, we identified 20 conserved M. oleifera miRNAs. For both these results an in silico analysis allowed us to predict some of their targets which in turn allowed us to link them to a wide range of physiological processes. Based on qRT-PCR expression analyses, we reported the expression profile of some selected conserved miRNAs in different M. oleifera tissues (roots, stems and leafs). We compared the most conserved miRNAs found in Moringa with those of other edible plants, such as Olea europaea and Brassica rapa. Furthermore, by taking advantage of a recently developed web- application based on an algorithm that compares plants and mammalian miRNAs, we identify a few possible plant miRNAs with functional homologies with mammalian ones. We used the 20 most abundant M. oleifera miRNAs to conduct a preliminary analysis to investigate potential cross-kingdom gene regulation. To our knowledge, this is the first report of M. oleifera miRNAs that uses high-throughput sequencing analysis. Our analysis increases the amount of information about plant miRNAs currently available and it can help us understanding the molecular mechanism of this medical plant. microRNA profile of M. oleifera seed, germinated on paper soaked in sterile water.
2015-07-01 | E-GEOD-70423 | biostudies-arrayexpress