Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of 5 to 7 days old Arabidopsis thaliana seedlings of wild type (Col-0) and the cytokinin deficient transgenic line 35S:CKX1

ABSTRACT: 5 to 7 days old Arabidopsis thaliana seedlings of wildtype (Col-0) and the cytokinin deficient transgenic line 35S:CKX1 (Werner et al. Plant Cell 15, 2532) at growth stage 1.00 (Boyes scale) grown in liquid medium were induced witn 5 µM 6-Benzylaminopurine for different periods of time in order to find cytokinin-related changes in gene expression.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Wolfram Brenner

PROVIDER: E-MEXP-344 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A morning-specific phytohormone gene expression program underlying rhythmic plant growth.

Michael Todd P TP Breton Ghislain G Hazen Samuel P SP Priest Henry H Mockler Todd C TC Kay Steve A SA Chory Joanne J

PLoS biology 20080901 9

Most organisms use daily light/dark cycles as timing cues to control many essential physiological processes. In plants, growth rates of the embryonic stem (hypocotyl) are maximal at different times of day, depending on external photoperiod and the internal circadian clock. However, the interactions between light signaling, the circadian clock, and growth-promoting hormone pathways in growth control remain poorly understood. At the molecular level, such growth rhythms could be attributed to sever ...[more]

PMID: 18798691

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Project description:Arabidopsis thaliana plants (ecotype Landsberg erecta) were grown at 20ËC 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 25ÂºC, 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 (22ÂºC, 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 For each time point (1h, 4h, 12h, and 24h) two biological replicates (DBM treatment) were performed. Control plants were harvested in parallel. Total RNA from each sample was used for two labelling reactions using dye-flips (Cy5 or Cy3) and labelled cDNA from treatment and control plants were co-hybridized. Thus, for each time-point four replicates were analyzed each comparing treatment with the corresponding control (rep1 and rep2 are dye-flips of biological replicate 1, and rep3 and rep4 are dye-flips of biological replicate 2). For background correction, we defined the mean of the lowest 10% of spot intensities from a particular subgrid as the background for that subgrid. This mean was subtracted from each spot in the subgrid. Signal intensities that did not exceed the background plus 3 standard deviations thereof were defined as not detectable and were excluded from further analyses. We normalized using loess curves thus generating log2 transformed expression ratios comparing DBM treatment with control. These ratios are given in the VALUE columns of each array.

Project description:Background: Banana (Musa) is one of the most important crops grown in tropical and sub-tropical areas. Cavendish, the most widely grown banana cultivar, is a triploid derived from an intra-species cross. Cavendish is relatively resistant to Race 1 of Fusarium oxysporum f. sp. Cubense (Foc1) which caused wide spread Panama disease during 1960s but is susceptible to Race 4 of Foc (Foc4) which has been causing epidemics in large areas of banana fields in Asia and Australia in the last decade and is threatening world banana production. The genome of the diploid species Musa acuminata (AA) which is the ancestor of a majority of cultivated banana has recently been sequenced. Availability of banana transcriptomes will be highly useful for improving banana genome annotation and assembly and for banana biological research. The knowledge of global gene expression patterns influenced by infection by different Foc races will help to understand the pathogenesis processes and the host responses to the infection. Results: RNA samples extracted from different organs of the Cavendish cultivar were pooled for deep sequencing using the Illumina sequencing technology. The assembled reads were aligned with the genome of M. accuminata and with sequences in the Genbank databases. The analysis led to identification of 842 genes that were not annotated by the Musa genome project. A large number of simple nucleotide polymorphisms (SNPs) and short insertions and deletion (indels) were identified from the transcriptome data. GFP-expressing Foc1 and Foc4 was generated and used to monitor the infection process. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. Both Foc1 and Foc4 were found to be able to invade banana roots and spread to root vascular tissues in the first two days following inoculation. The profiling analysis revealed that inoculation with Foc1 and Foc4 caused similar changes in the gene expression profiles in the infected banana roots. The Foc infection led to induction of many well-known defense-related genes including PATHOGENESIS-RELATED 5 (PR5), PAL, and a lignin-forming peroxidase. The WRKY40 gene, which is a negative regulator of the defense pathway in Arabidopsis, was quickly and strongly suppressed by the infection. Two genes encoding the ethylene biosynthetic enzyme ACC oxidase and several ethylene-responsive transcription factors were among strongly induced genes by both Foc1 and Foc4 Conclusions: Both Foc1 and Foc4 are able to spread into the vascular system of banana roots during the first two days of the infection process and their infection led to similar gene expression profiles in banana roots. The transcriptome profiling analysis indicates that the ethylene synthetic and signalling pathways were activated in response to the Foc infection. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. The plants whose roots were immersed in the culture medium without the pathogen (mock inoculation) were used as a control.

Dataset Information

Transcription profiling of 5 to 7 days old Arabidopsis thaliana seedlings of wild type (Col-0) and the cytokinin deficient transgenic line 35S:CKX1

Publications

A morning-specific phytohormone gene expression program underlying rhythmic plant growth.

Similar Datasets

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