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Circadian rhythms of sense and antisense transcription in a highly polyploid crop.

ABSTRACT: Sugarcane plants were grown in soil in a 12h light/ 12h dark photoperiod and 26oC for 3 months. Then, the plants were transferred to constant light conditions and 24 h later, leaves were harvested every 4 h for 48 h.

ORGANISM(S): Saccharum hybrid cultivar (mixed) Saccharum officinarum

PROVIDER: GSE42725 | GEO | 2013/11/21

SECONDARY ACCESSION(S): PRJNA183017

REPOSITORIES: GEO

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Circadian rhythms of sense and antisense transcription in a highly polyploid crop.

Project description:Sugarcane plants were grown in soil in a 12h light/ 12h dark photoperiod and 26oC for 3 months. Then, the plants were transferred to constant light conditions and 24 h later, leaves were harvested every 4 h for 48 h. Samples were collected from 24 h in constant light to 68 h in constant light and were labelled accordingly. Two biological replicates of each time point were made, with a dye swap with the reference. The reference used was a equimolar solution of all samples.

2013-11-21 | E-GEOD-42725 | biostudies-arrayexpress

Circadian rhythms of sense and antisense transcription in sugarcane, a highly polyploid crop.

Project description: Not available

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Expansion of the circadian transcriptome in Brassica rapa supports genome wide diversification of homeolog gene expression patterns

Project description:Following divergence from Arabidopsis thaliana, Brassica rapa underwent a whole genome triplication followed by extensive genome fractionation. Preferential retention of circadian clock genes suggest that expansion of the circadian network may play an important role during B. rapa domestication. To characterize the circadian transcriptome network, RNA-seq was performed in the B. rapa oil-type variety R500 following photocycle and thermocycle circadian time courses. The photocycle (LDHH) time course consisted of growing plants for 15 days at 20°C under a 12h light/12h dark photoperiod and transfering plants to constant light and 20°C 24h prior to harvesting leaf tissue every 2h for 48h starting at ZT24 with 2 biological replicates at every time point. The thermocycle (LLHC) time course consisted of growing plants for 15 days under constant light with a 12h 20°C/12h 10°C thermoperiod and transfering plants to constant light and 20°C 24h prior to harvesting leaf tissue every 2h for 48h starting at ZT24 with 2 biological replicates at every time point.

2020-01-31 | GSE123654 | GEO

pICln, an spliceosome assembly chaperone, controls alternative splicing, flowering time and stress responses in Arabidopsis

Project description:RNA-Seq from picln-1 mutant, prmt5-5 mutant and wt grown at 22°C for 9 days in a 12h light 12h dark photoperiod

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Diamond Back Moth treatment

Project description:Arabidopsis thaliana plants (ecotype Landsberg erecta) were grown at 20˚C constant temperature, 8 hr/16 hr Light/Dark photoperiod at 50-60% ambient humidity, for 8 to 9 weeks. Short day conditions prevented the onset of flowering and the plants were thus maintained in growth stage 1 (leaf production) with 13 to 15 rosette leaves larger than 1mm (stage 1.13 to 1.14). Diamondback moth (DBM, Plutella xylostella) larvae were maintained on cabbage (Brassica oleracea) plants in a climate-controlled room at 25ºC, 12 hr photoperiod with 50%-60% relative humidity. Two days before exposing A. thaliana plants to herbivore treatment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod). For insect treatment, seven Diamondback moth (DBM, Plutella xylostella) larvae (third to fifth instars) were placed on a group of four or five plants until time of harvest, for each time point separately. All rosette leaves were harvested at 1h, 4h, 12h, and 24h after onset of continuous herbivory and flash frozen in liquid nitrogen. Control plants were maintained under the same conditions and harvested in parallel. Keywords: time course, stress response, herbivory response

2008-03-04 | GSE10681 | GEO

Cell cycle and cell death interaction in plants: PCNA, AtXRs and AtMIPS pathway.

Project description:rs07-04_mips - atmips mutant/photoperiod - In Arabidopsis thaliana, how does MIPS knock out influence gene expression? In AtMIPS mutants how does photoperiod influence gene expression. - Wild type Colombia and MIPS mutant (Salk 023626) plants are grown in short days (8h light) during 27 days and then transfered in long days (16h light) during 4 days. J4JC correspond to 27+4=31 days plants in short days. Keywords: gene knock out

2009-03-07 | GSE15123 | GEO

Diurnal transcriptome rhythms in mice with genetically ablated clock function in the suprachiasmatic nucleus (SCN)

Project description:Male KO (Syt10-Cre/Cre x Bmal1-flox/-) and CON (Syt10-Cre/Cre x Bmal1-+/-) mice were entrained to 12h:12h light:dark conditions for two weeks and sacrificed at 4 different time points (CT1, 7, 13, 19) on the second day after release into constant darkness conditions. Total RNA was isolated from epididymal white adipose tissue biopsies and subjected to microarray hybridization.

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The transcriptomic landscape of the photoperiodic stress response in Arabidopsis thaliana resembles the response to pathogen infection

Project description:Plants are exposed to regular diurnal rhythms of light and dark. Changes in the photoperiod by the prolongation of the light period cause photoperiod stress in short day-adapted Arabidopsis thaliana. Here we report on the transcriptional response to photoperiod stress of wild-type A. thaliana and photoperiod stress-sensitive cytokinin signaling and clock mutants. Transcriptomic changes induced by photoperiod stress included numerous changes in reactive oxygen species (ROS)-related transcripts and showed a strong overlap with alterations occurring in response to ozone stress and pathogen attack, which have in common the induction of an apoplastic oxidative burst. A core set of photoperiod stress-responsive genes has been identified, including salicylic acid (SA)-biosynthesis and -signaling genes. Genetic analysis revealed a central role for NPR1 in the photoperiod stress response as npr1-1 mutants were stress-insensitive. Photoperiod stress treatment led to a strong increase in camalexin levels which is also observed in response to pathogen infections. Photoperiod stress induced the resistance of Arabidopsis plants to a subsequent infection by Pseudomonas syringae pv. tomato DC3000 indicating priming of the defence response. Together, photoperiod stress causes transcriptional reprogramming resembling plant pathogen defence responses and induces systemic acquired resistance in the absence of a pathogen.

2022-02-28 | GSE173899 | GEO

Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [WGBS]

Project description:We establish global maps of regulatory elements and chromatin states and their dynamics, for both the whole and subgenomes of four tissue types (young leaf, flower bud, silique, and root) of two B. napus lines. Approximately 52 % of the genome was annotated with different epigenomic signals. We also uncover a new bivalent chromatin state in B. napus and suggest its key roles in regulating tissue-specific gene expression. Furthermore, we observe that different types of duplicated genes have differential patterns of histone modifications, DNA methylation, and selection pressures. Together, we provide valuable epigenetic data resources of allopolyploid B. napus and reveal the central role of epigenomic information in understanding transcriptional regulation in polyploid plants.

2021-01-31 | GSE143285 | GEO

Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [RNA-seq]

2021-01-31 | GSE143286 | GEO

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