Ontology highlight
ABSTRACT:
PROVIDER: PRJNA835980 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19145406_1.fastq.gz | Fastqsanger.gz | |||
| SRR19145406_2.fastq.gz | Fastqsanger.gz | |||
| SRR19145407_1.fastq.gz | Fastqsanger.gz | |||
| SRR19145407_2.fastq.gz | Fastqsanger.gz | |||
| SRR19145408_1.fastq.gz | Fastqsanger.gz |
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Project description:Description of gene expression in various types of cauliflower (including Romanesco type) Cauliflower structures develop on inflorescences from plants such as the apetala1 cauliflower double mutant in Arabidopsis thaliana or in the edible Brassica oleracea var botrytis or Romanesco. Whereas the genetic basis for the development of such structure is well understood in the model plant Arabidopsis thaliana, it is less understood in Brassica oleracea. In order to gain insight into the gene expression present in cauliflower and Romanesco curds, we performed RNA-seq analyses of mature cauliflowers and Romanesco curds and from growing cauliflowers curds. This analysis allowed to establish the nature of genes from the APETALA1 and CAULIFLOWER clade that are either mutated or expressed at very low levels in curd structures. These results shed light on the molecular nature of structures that have been selected in the domestication process.
2021-06-30 | GSE150627 | GEO
Project description:We investigated the expression profiles and genomic organization of PP2Cs-encoding genes in Brassica oleracea. Analysis of cDNA macroarray transcription profiles for Brassica oleracea and Arabidopsis thaliana revealed significant differences in the expression of a gene encoding protein phosphatase 2C, ABI1, a member of the group A PP2C. To gain insight into the ABA signaling network conservation in a model plant and its crop relatives group A PP2C genes in B. oleracea have been identified and functionally characterized. Twenty homologous sequences were identified as putative members of the group A PP2Cs (BolC.PP2Cs). Phylogenetic analysis revealed that the B. oleracea homologues are closely related to the particular members of the A. thaliana PP2C family. The genetic analysis has corroborated the presence of 2 to 3 copies for almost all of the PP2Cs examined, which corresponded to the unique genes in the A. thaliana genome. Gene expression analyses showed that among 15 PP2Cs-encoding genes studied in B.oleracea, BolC.ABI2, BolC.HAB1, BolC.HAB2.a-c, and BolC.PP2CA.a were drought-induced. However, in contrary to AtPP2Cs, only BolC.ABI1.a-b, BolC.ABI2 and BolC.PP2CA.a were ABA-responsive at the time points tested. Our results indicate that in B. oleracea PP2C-based drought stress signaling has evolved distinctly in comparison to A. thaliana. It is hypothesized that different reactions of particular B. oleracea PP2C genes to the water stress and ABA treatment may indicate lower conservation of their specificity in stress-induced reversible phosphorylation-based protein network operating in B. oleracea and A. thaliana.
2012-10-28 | GSE39753 | GEO
Project description:Deep sequencing of mRNA from seven different tissues of Brassica oleracea Analysis of ploy(A)+ RNA of multiple different tissues of Brassica oleracea containing Bud, Callus, Root, Stem, Leaf, Flower and Silique.
2014-05-27 | E-GEOD-42891 | biostudies-arrayexpress
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.
2009-05-03 | GSE15915 | GEO
Project description:We investigated the expression profiles and genomic organization of PP2Cs-encoding genes in Brassica oleracea. Analysis of cDNA macroarray transcription profiles for Brassica oleracea and Arabidopsis thaliana revealed significant differences in the expression of a gene encoding protein phosphatase 2C, ABI1, a member of the group A PP2C. To gain insight into the ABA signaling network conservation in a model plant and its crop relatives group A PP2C genes in B. oleracea have been identified and functionally characterized. Twenty homologous sequences were identified as putative members of the group A PP2Cs (BolC.PP2Cs). Phylogenetic analysis revealed that the B. oleracea homologues are closely related to the particular members of the A. thaliana PP2C family. The genetic analysis has corroborated the presence of 2 to 3 copies for almost all of the PP2Cs examined, which corresponded to the unique genes in the A. thaliana genome. Gene expression analyses showed that among 15 PP2Cs-encoding genes studied in B.oleracea, BolC.ABI2, BolC.HAB1, BolC.HAB2.a-c, and BolC.PP2CA.a were drought-induced. However, in contrary to AtPP2Cs, only BolC.ABI1.a-b, BolC.ABI2 and BolC.PP2CA.a were ABA-responsive at the time points tested. Our results indicate that in B. oleracea PP2C-based drought stress signaling has evolved distinctly in comparison to A. thaliana. It is hypothesized that different reactions of particular B. oleracea PP2C genes to the water stress and ABA treatment may indicate lower conservation of their specificity in stress-induced reversible phosphorylation-based protein network operating in B. oleracea and A. thaliana. For each genotype 7 samples were analysed; 4 controls and 3 samples extracted from drought-treated plants. The reliability and reproducibility of the macroarray analyses were ensured by using biological replicates in the experiment.
2012-10-28 | E-GEOD-39753 | biostudies-arrayexpress
Project description:Purpose: We conducted an evolutionary-based genome-wide analysis of the MYB-CC gene family in Brassica species. Methods: B. napus (accession Zhongshuang11) was kindly provided by the Oilcrops Research Institute, Chinese Academy of Agricultural Sciences. The seeds were disinfected in 70% ethanol for 1 min, washed with ddH2O three to four times, placed on a petri dish lined with two layers of filter paper, and then germinated at 24oC in growth chamber. After three days, the germinated seedlings were transferred to MS medium containing 0.3% agar and 3% sucrose at pH 5.7. The seedlings grew at 24oC under a long-day light cycle (16 h light/8 h dark) and a relative humidity of 65%. Then the two-week-old plants were cultured in 1 mM and 1 μM Pi liquid medium for 24 h, respectively. Rapeseed seedlings’ shoots and roots were collected and frozen in liquid nitrogen. The RNA-seq analysis was carried out by Biomarker (Beijing). A total of 16 RNA samples were sequenced using the Illumina HiSeq 2,000 platform (Illumina, USA). Results: The position of the MYB-CC genes was investigated according to the B. napus database (http://www.genoscope.cns.fr), the B. oleracea genome database (http://www.ocri-genomics.org), and the Brassica database (BRAD, http://brassicadb.org), respectively. MapInspect software was used to locate the MYB-CC genes. The gene duplication was defined as: a coverage region between two sequences of more than 70% with more than 85% similarity in the coverage region (Zhou et al., 2004; Yang et al., 2008). Additionally, the ka (non-synonymous mutation rate) and ks (synonymous mutation rate) values of the repeating gene pairs were calculated using DnaSp software. Conclusions:This study comprehensively evaluated the identification, classification, expression and evolution analyses of MYB-CC gene family of Brassica species. A total of 30, 34, and 55 MYB-CC genes were identified in B. rapa, B. oleracea, and B. napus, respectively. All of the MYB-CC genes were divided into nine groups in the phylogenetic tree. Members of the same group have similar gene structures and conserved motifs, indicating that they could be conserved during evolution. In Brassica, WGT and allotetraploidy were vital for the expansion of MYB-CC genes.
2022-01-25 | GSE192452 | GEO
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes. Four-condition experiment, comparison of transcription profiles of the genomes. Four biological replicates were used, independently grown and harvested. One replicate per array.
2010-05-19 | E-GEOD-15915 | biostudies-arrayexpress
Project description:Gene expression changes during the initial stages of black spot disease caused by Alternaria brassicicola on Brassica oleracea (Brassica oleracea var. capitata f. alba, white cabbage) leaves were investigated with Arabidopsis thaliana oligonucleotide microarrays. Transcriptional profiling of infected B. oleracea leaves revealed that photosynthesis was the most negatively regulated biological process. The negative regulation of 6 photosynthesis-related genes, mainly the genes involved in the photosynthesis light reaction and Calvin cycle, was observed as early as 12 hours post infection (hpi). It progressed through 48-hpi stage, when 44 down-regulated photosynthesis-related genes were detected. The analyses of infected leaves at microscopic, ultrastructural and physiological levels supported the microarray-based observations and indicated that the photosynthetic processes are suppressed in B. oleracea as a result of the fungal infection.
2020-07-25 | GSE155051 | GEO
Project description:Deep sequencing of mRNA from seven different tissues of Brassica oleracea
2014-05-27 | GSE42891 | GEO
Project description:Heterologous expression of a water soluble chlorophyll protein from Brassica oleracea var. gemmifera in the phototrophic purple bacterium Rhodobacter sphaeroides was verified by bottom-up proteomic analysis.
2016-07-12 | PXD002638 | Pride