Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1161144 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30668300_1.fastq.gz | Fastqsanger.gz | |||
| SRR30668300_2.fastq.gz | Fastqsanger.gz | |||
| SRR30668295_1.fastq.gz | Fastqsanger.gz | |||
| SRR30668295_2.fastq.gz | Fastqsanger.gz | |||
| SRR30668296_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome analysis of axillary buds in Ginkgo biloba
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Project description:Shoot branching of flowering plants exhibits phenotypic plasticity and variability. This plasticity is determined by the activity of axillary meristems, which in turn is influenced by endogenous and exogenous cues such as nutrients and light. In many species, not all buds on the main shoot develop into branches despite favorable growing conditions. In petunia, basal buds (buds 1-3) typically do not grow out to form branches, while more apical buds (buds 6 and 7) are competent to grow. The genetic regulation of buds was explored using transcriptome analyses of petunia axillary buds at different positions on the main stem. To suppress or promote bud outgrowth, we grew the plants in media with differing phosphate (P) levels. Using RNA-seq, we found many (>5000) differentially expressed genes between bud 6 or 7, and bud 2. In addition, more genes were differentially expressed when we transferred the plants from low P to high P medium, compared with shifting from high P to low P medium. Buds 6 and 7 had increased transcript abundance of cytokinin and auxin-related genes, whereas the basal non-growing buds (bud 2 and to a lesser extent bud 3) had higher expression of strigolactone, abscisic acid, and dormancy-related genes, suggesting the outgrowth of these basal buds was actively suppressed. Consistent with this, the expression of ABA associated genes decreased significantly in apical buds after stimulating growth by switching the medium from low P to high P. Furthermore, comparisons between our data and transcriptome data from other species suggest that the suppression of outgrowth of bud 2 was correlated with a limited supply of carbon to these axillary buds. Candidate genes that might repress bud outgrowth were identified by co-expression analysis.
2023-07-26 | GSE237985 | GEO
Project description:Arabis alpina, similar to woody perennials, has a complex architecture with a zone of axillary vegetative branches and a zone of dormant buds that serve as perennating organs. We show that floral development during vernalization is the key for shaping the dormant bud zone by facilitating a synchronized and rapid growth after vernalization and thereby causing an increase in auxin transport, response and endogenous indole-3-acetic acid (IAA) levels in the stem. Floral development during vernalization is associated with the development of axillary buds in subapical nodes. Our transcriptome analysis indicated that these buds are not dormant during vernalization but only reach sustained growth after the return to warm temperatures. Floral and subapical vegetative branches grow after vernalization and inhibit the development of the buds below. Dormancy in these buds is regulated across the A. alpina life cycle by low temperatures and by apical dominance in a BRANCHED 1 dependent mechanism.
2020-03-01 | GSE126944 | GEO
Project description:Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. In this study, we employed next-generation sequencing, gene expression analysis and metabolite profiling to identify sRNAs and quantify distinct hormones, respectively, in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.). Differential accumulation of abscisic acid (ABA), gibberellins (GA), and cytokinins indicates a dynamic balance of these hormones during sugarcane bud outgrowth. A number of repeat-associated siRNAs generated from distinct transposable elements and genes were highly expressed in both inactive and developing buds. RT-qPCR results revealed that specific miRNAs were differentially expressed in developing buds and some correlate negatively with the expression of their targets. Expression patterns of miR159 and its experimentally confirmed target GAMYB suggest they play roles in regulating ABA and GA-signaling pathways during bud outgrowth. Our work reveals, for the first time, differences in composition and expression profiles of small RNAs and targets between inactive and developing buds that, together with the endogenous balance of specific hormones, may be important to regulate axillary bud outgrowth in plants.
2012-12-31 | GSE38894 | GEO
Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohoromones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array
2009-11-18 | GSE18987 | GEO
Project description:Purpose: observe the difference between potato (Solanum tuberosum ssp. andigena) WT and BRC1b RNAi axillary buds in response to the transition from long-day to short-day conditions. The time course includes four time points: Long days, after 2 days in short days, 1 week in short days and 2 weeks in short days. Methods: stem were flash-frozen in N2(l) one hour after dawn and the axillary buds were dissected in the cold room. The four axillary buds bellow the third visible node counting from the apex (those most likely to produce tubers in RNAi line) were collected. RNA was extracted with FavorPrep™ Plant Total RNA Mini Kit from FAVORGEN. DNA was degraded in the column with RNase-free DNase I (Roche). Three biological replicates were used and each replicate is a pool of axillary buds from 4 plants.
2022-01-30 | GSE155774 | GEO
Project description:The aim of this study is to identify genes differentially expressed during the transition between dormancy and activity in axillary shoot apical meristems. We have chosen to study this by comparing mRNA populations from the axillary buds of the auxin over-responding, apically dominant axr3-1 mutant of Arabidopsis,with those from the axillary buds of the auxin resistant axr1-12 bushy mutant. Preliminary investigation using cDNA AFLP has been successful in identifying differentially expressed transcripts in the buds of these two genotypes, thus demonstrating the importance of this study, however this is a time consuming procedure. Axillary buds from axr3-1 are seen to arrest at an early stage when the buds are approximately 2mm long and harvested at this point. Buds of a similar size were harvested from axr1-12 plants and the RNA extracted using Qiagen columns.These two mRNA samples will represent the dormant and active buds to be comparedin this experiment. The plants from which these buds were harvested were grown in adjacent p40 trays in a plant growth room. Between two and three buds were harvested from each plant.
2003-10-20 | E-NASC-10 | biostudies-arrayexpress
Project description:The aim of this study is to identify genes differentially expressed during the transition between dormancy and activity in axillary shoot apical meristems. We have chosen to study this by comparing mRNA populations from the axillary buds of the auxin over-responding, apically dominant axr3-1 mutant of Arabidopsis,with those from the axillary buds of the auxin resistant axr1-12 bushy mutant. Preliminary investigation using cDNA AFLP has been successful in identifying differentially expressed transcripts in the buds of these two genotypes, thus demonstrating the importance of this study, however this is a time consuming procedure. Axillary buds from axr3-1 are seen to arrest at an early stage when the buds are approximately 2mm long and harvested at this point. Buds of a similar size were harvested from axr1-12 plants and the RNA extracted using Qiagen columns.These two mRNA samples will represent the dormant and active buds to be comparedin this experiment. The plants from which these buds were harvested were grown in adjacent p40 trays in a plant growth room. Between two and three buds were harvested from each plant. Experimenter name: Sally Ward Experimenter phone: 01904 328683 Experimenter fax: 01904 328682 Experimenter institute: University of York Experimenter address: Dept of Biology (Area 11), University of York, Heslington, York Experimenter zip/postal_code: YO10 5DD Experimenter country: UK Keywords: genetic_modification_design
2008-01-31 | GSE10324 | GEO