Differential gene expression during floral transition in pineapple.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA999438 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25443600_1.fastq.gz | Fastqsanger.gz | |||
| SRR25443600_2.fastq.gz | Fastqsanger.gz | |||
| SRR25443601_1.fastq.gz | Fastqsanger.gz | |||
| SRR25443601_2.fastq.gz | Fastqsanger.gz | |||
| SRR25443602_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Differential Gene Expression During Floral Transition in Pineapple
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Project description:Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 hours to 8 days after treatment, 7,961 genes were found to exhibit differential expression (DEG) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS (CO), a WUSCHEL gene, two APETALA1/FRUTFULL (AP1/FUL) genes, an epidermal patterning gene and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2) and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated in the apex and not the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads acts directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP and AP2.
2023-11-22 | GSE239489 | GEO
Project description:Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 hours to 8 days after treatment, 7,961 genes were found to exhibit differential expression (DEG) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS (CO), a WUSCHEL gene, two APETALA1/FRUTFULL (AP1/FUL) genes, an epidermal patterning gene and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2) and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated in the apex and not the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads acts directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP and AP2.
2023-11-22 | GSE241286 | GEO
Project description:transition-Transcriptome of floral transition
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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: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.
2019-04-17 | GSE116123 | GEO
Project description:The main objective of the present study was to identify citrus transcrition factors putatively involved in the juvenile to adult transition in citrus. A oligonucleotide microarray containing 1152 putative unigenes of citrus transcription factors was used. Pineapple sweet orange (C. sinensis (L.) was analyzed in two diferent developmental stages, junenile and adult. Four replicates for each sample category were generated and for each genotipe juvenile versus adult samples were compared . Comparative transcriptomic hybridization
2013-07-27 | E-GEOD-39799 | biostudies-arrayexpress
Project description:Peel color is a key factor that affects the fruit’s aesthetic and economic values. In Red Sugar pineapple, the peels’ red color reduces during maturation. Limited knowledge is available on the regulation of pineapple peel discoloration, which makes it important to study the molecular mechanisms associated with this important trait. Here, we report that a decrease in anthocyanin biosynthesis is predominantly associated with the pineapple peel color change during maturation. Particularly the exclusive accumulation of cyanidin in 60 days after flowering (DAF) as compared to 120 DAF gives the fruit peel its distinct reddish color. Our findings suggest that the changes in the expression of key structural genes (early and late biosynthetic genes) of the anthocyanin (cyanidin) biosynthesis pathway are responsible for peel discoloration. Based on a gene co-expression analysis and a transient expression, we identified two transcription factors i.e., AcHOX21 and AcMYB12, and showed that their downregulation leads to the reduced anthocyanin accumulation with fruit maturation.
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Project description:Bisulfite treatment libraries were made to characterize the DNA methylome of pineapple
2018-09-27 | GSE120401 | GEO
Project description:The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.v
2019-09-09 | PXD009794 | Pride