Ontology highlight
ABSTRACT:
PROVIDER: PRJNA815882 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18319851_1.fastq.gz | Fastqsanger.gz | |||
| SRR18319851_2.fastq.gz | Fastqsanger.gz | |||
| SRR18319852_1.fastq.gz | Fastqsanger.gz | |||
| SRR18319852_2.fastq.gz | Fastqsanger.gz | |||
| SRR18319853_1.fastq.gz | Fastqsanger.gz |
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Project description:Orchid Dendrobium Sonia (Sonia) has wide demand in floral market throughout the world due to its vibrant coloured flowers, flowering recurrence and dense inflorescence. Effects of different monochromatic light qualities (red, far-red, blue, white) on different developmental and growth responses such as seed gemination, shoot and root growth, chlorophyll and carotenoid accumulation were studied in Sonia. Asymbiotic seed germination was the highest under blue or white light (80%, p<0.001) and least under far-red (55%, p<0.001) suggesting that it could either be controlled by an exceptional novel function of Cryptochrome 1 or the blue wavelengths perceived by PHYA or PHYB in Sonia. All analyses were done in 6-months-old plants till 1 year of age. Shoot length increased significantly in white or red light (3.7-fold, 3.5-fold respectively) while was least under far-red (decreased by 1.6-fold) indicating the major regulatory role of PHYB for shoot growth. Root growth in red in Sonia was more similar to hypocotyl adventitious root (HAR) formation genetically considering PHYB transcript expression. We suggest that the root growth (HAR) under red in Sonia is partly attributed to PHYB, negatively regulated with HY5 transcription factor and positively associated with auxin biosynthesis and accumulation gene BABY BOOM (BBM2) and efflux carriers such as LIKE AUXIN RESISTANT 2 and 3 (LAX2, LAX3). Highest chlorophyll content under far-red and blue might be a hyper-response of SAR under FR light in Sonia. Taxonomic tree analysis finds Sonia closer to Phalenopsis and Dendrobium catenatum Lindl. The three phytochromes and one cryptochrome sequences which were similar to PHYA, B, C and CRY1 respectively. CRY1 was retrieved with one more isoform CRY1_X2, with all these sequences more similar to those of Oryza.sativa. Further study can clarify the indicating reason of a probable gene loss which is evident from the absence of any sequence similar to CRY2 in root RNA isolates of Dendrobium Sonia.
2024-03-01 | GSE252123 | GEO
Project description:Dendrobium catenatum (D. catenatum) has long been used as an important medicinal herb in oriental medicine. Polysaccharide, flavonoid, and alkaloid are the major active ingredients, the production and accumulation of which are frequently affected by many environmental factors including water, temperature, and mycorrhizal fungus. However, how phytohormones frequently used in orchid tissue culture regulate the production of active components in D. catenatum is far from clear. Here, major medicinal metabolites were comparatively analyzed in 2-month-old D. catenatum seedlings exposed to phytohormones (0.1 mg/L NAA and/or 1.0 mg/L 6-BA) for three weeks, and eight transcriptomes (two replicates each) corresponding to the treatments were generated. Results demonstrated that the phytohormones triggered transcriptional reprograming, analysis of which revealed a tight association of β-glucosidase (BGLU) expression with the accumulation of polysaccharide. Subsequently, a second RNA-sequencing was further conducted to reveal that a relatively short period (2 w) of varied concentrations of 6-BA application might initially reduce BGLU expression and polysaccharide content and then increase their levels with prolonged treatments (4 w). The RNA-seq data was reconfirmed by functional analysis that 6-BA induced polysaccharide production, while knockdown of BGLU2L resulted in decreased polysaccharide levels. Therefore, the present study clearly demonstrated that BGLU is a key regulator for polysaccharide production and that it is extremely susceptible to NAA and 6-BA treatments in D. catenatum.
2022-05-31 | GSE184090 | GEO
Project description:This model is from the article:
The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development
Muraro D, Byrne H, King J, Voss U, Kieber J, Bennett M.
J Theor Biol.2011 Aug 21;283(1):152-67.
PMID: 21640126,
Abstract:
Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations.
2024-09-02 | BIOMD0000000416 | BioModels
Project description:Root architecture is vital for plant growth and largely depends on primary root growth and lateral root development. Several plant hormones have been shown to affect root architecture among which auxin has been granted a central role. Lately, small signalling peptides also emerged as potential molecular components regulating root growth and development. Here, we identified C-TERMINALLY ENCODED PEPTIDE 5 (CEP5) as a novel, phloem poleexpressed paracrine signal for lateral root initiation. Our genetic, biochemical and pharmacological results show that CEP5 counteracts auxin signalling by stabilizing AUXIN/INDOLE ACETIC ACID (AUX/IAA) transcriptional repressors, suggesting the existence of an additional control mechanism through which plants can attenuate auxin signalling in a developmental context. Reducing CEP5 expression levels resulted in an increased auxin response and subsequently interfered with the normal progression through lateral root developmental stages.
2022-03-01 | PXD002589 | Pride
Project description:Dendrobium catenatum Genome sequencing and assembly
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Project description:Dendrobium catenatum Genome sequencing and assembly
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