Floral transition trajectories dissected by single meristem transcriptomes at high temporal resolution.
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ABSTRACT:
PROVIDER: PRJNA702436 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13730548_1.fastq.gz | Fastqsanger.gz | |||
| SRR13730548_2.fastq.gz | Fastqsanger.gz | |||
| SRR13730549_1.fastq.gz | Fastqsanger.gz | |||
| SRR13730549_2.fastq.gz | Fastqsanger.gz | |||
| SRR13730550_1.fastq.gz | Fastqsanger.gz |
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Project description:We developed a method we denote as single meristem transcriptome profiling (SMT) and utilize it in this work to analyze hundreds of single tomato shoot-apical-meristems of several genotypes, which were collected during or when approaching floral transition. This provide us with dense temporal sampling of the wild-type process which we used in order to generate a pseudo-time reference, anchored by morphology-based scores. This allows for examination of molecular changes in the genetically-perturbed processes by temporal alignment.
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Project description:Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that mediate floral transition in the shoot apical meristem. Many characterized mutations disrupt these environmental responses, but downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant impaired in several environmental pathways and showed that it possesses severely reduced flowering responses to changes in photoperiod and ambient temperature. RNA-seq analysis of the quintuple mutant showed that the expression of genes encoding gibberellin biosynthesis enzymes and transcription factors involved in the age pathway correlates with flowering. Mutagenesis of the quintuple mutant generated two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The mutated genes were identified by isogenic mapping and transgenic complementation. The qem1 mutant was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, the qem2 mutation is in CHROMATIN REMODELING 4 (CHR4), which has not been genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 mediates the response to endogenous flowering pathways in the inflorescence meristem to promote floral identity.
2020-03-02 | PXD016457 | Pride
Project description:We sequenced cDNA synthesized from mRNA from 3 time points of a time course of Arabidopsis thaliana shoot apical meristems. Plants were grown two weeks in short days (time point +0LD) and then exposed to long days for 1 day (time point +1LD) and 3 days (time point +3LD). Meristem cells were collected using laser capture microdissection, to generate a meristem-specific time course of gene expression in the early stages of floral induction. The experiment was done in three biological replicates (called A, B, and C). Some repetitions of sequencing on a few samples (technical replicates) were also done Examination of mRNA levels in shoot apical meristems at 3 time points from the stage of vegetative meristem to the stage of a transition meristem, before the formation of floral meristems.
2012-02-01 | E-GEOD-34476 | biostudies-arrayexpress
Project description:We sequenced cDNA synthesized from mRNA from 3 time points of a time course of Arabidopsis thaliana shoot apical meristems. Plants were grown two weeks in short days (time point +0LD) and then exposed to long days for 1 day (time point +1LD) and 3 days (time point +3LD). Meristem cells were collected using laser capture microdissection, to generate a meristem-specific time course of gene expression in the early stages of floral induction. The experiment was done in three biological replicates (called A, B, and C). Some repetitions of sequencing on a few samples (technical replicates) were also done
2012-02-01 | GSE34476 | GEO
Project description:ngs2015_01_transition-transition-Identification of transcripts and long non-coding transcripts in wild-type mature rosette leaves of Arabidopsis thaliana during a photoperiodic switch inducing floral transition.-Arabidopsis thaliana Col-0 plants were grown in soil, in growth chamber under white fluorescent light, under short-day (8 hours light/16 hours dark, SD) or long-day (16 hours light/8 hours dark, LD) conditions. Temperature in SD was 21°C during the light period and 18°C during the dark, humidity (65%) remained constant. In LD, temperature (21°C) and humidity (70%) remained constant. Plants were cultured for 4 weeks in individual pot, in SD then transferred in LD. Plants were analysed at different time points before transfer (T0) and after two, three and five days of transfer (T2, T3, T5). The second pair of leaves was collected before dusk, at Zeitgeber time 15 (ZT15) considering ZT 0 the switched on of the light. Three biological replicates were performed. The floral transition occurs between T0 and T5 based on AP1:GUS marker, a inflorescence meristem is not yet visible during this developmental window at the center of the rosette.
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Project description:The current experiment was designed to obtain a broad characterization of the genetic pathways acting in early Aquilegia coerulea floral meristem development. We conducted an in-depth transcriptome profiling of early floral development in A. coerulea at four finely dissected developmental stages, with eight biological replicates per stage. . The developmental window we sequenced sampled stages that started with a late phase of stamen initiation, covered the period of FM termination, and ended with the initial stage of morphogenesis of the floral organs.
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2018-05-04 | GSE113894 | GEO
Project description:The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. In this study, we addressed the nature of SAM gene networks involved in the early floral initiation process in the crop legume soybean. Unique aspects (such as pod development and nitrogen fixation) of legume development make them appealing for plant development studies. Soybean, a major oilseed crop, possesses varied maturity groups; hence, understanding and unravelling initial transition control has implications in manipulating crop yield. To this end, we performed global gene expression analysis using Affymetrix® soybean GeneChip® with RNA isolated from micro-dissected soybean SAMs at various time points after plants were shifted from long-day to short-day growth conditions. Analysis of the resulting microarray data revealed a total of 331 transcripts that have differential expression profiles. Intriguingly, about 20% of the transcripts affected by the switch in the development program have orthologs reported to be responsive to abscisic acid (ABA), suggesting an increase in ABA levels in the SAM during this developmental change. A subsequent immunoassay verified this, thereby implicating its possible function as an endogenous signal during the floral evocation process. The striking occurrence of abiotic stress-related transcripts, including trehalose metabolism genes, in SAMs during the early transition to floral meristems points to an overlap of abiotic stress and floral signalling pathways in soybean. In addition, other hormones - auxin, jasmonic acid and brassinosteroids - and a number of candidate protein kinases may also act in the signalling process prior to or concurrently with the induction of the putative floral homeiotic transcripts. This indicates that molecular events mediated by multiple hormonal pathways are part of the mechanism employed by soybean to regulate the floral transition process. Keywords: transcript profiling floral transition soybean shoot apical meristem
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