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Time course transcriptomic analysis of cabbage (Brassica oleracea ssp. capitala L.) during vernalization

ABSTRACT: Time course transcriptomic analysis of cabbage (Brassica oleracea ssp. capitala L.) during vernalization

PROVIDER: PRJNA954884 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24150001_1.fastq.gz	Fastqsanger.gz
	SRR24150001_2.fastq.gz	Fastqsanger.gz
	SRR24150002_1.fastq.gz	Fastqsanger.gz
	SRR24150002_2.fastq.gz	Fastqsanger.gz
	SRR24150003_1.fastq.gz	Fastqsanger.gz

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Time course transcriptomic analysis of cabbage (Brassica oleracea ssp. capitala L.) during vernalization

Project description:We report here NGS RNA-seqencing datasets for three different vernalization time course of Brassica oleracea plants

2023-04-17 | GSE229562 | GEO

Whole-transcriptome analysis and construction of vernalization-related ceRNA-miRNA-target gene regulatory network in Chinese cabbage (Brassica campestris L. ssp. pekinensis) [seed miRNA]

Project description:The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering. Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.

2021-11-17 | GSE171708 | GEO

Whole-transcriptome analysis and construction of vernalization-related ceRNA-miRNA-target gene regulatory network in Chinese cabbage (Brassica campestris L. ssp. pekinensis) [seed mRNA]

2021-11-17 | GSE171707 | GEO

Identification of flowering time genes associated with vernalization in Chinese cabbage and their differential expression in radish

Project description:We conducted genome-wide transcriptome analysis using the inbred Chinese cabbage line, ‘4004’, which displayed early flowering in response to vernalization. A total of 1,677 differentially-expressed genes (DEGs) were identified with and without vernalization. Transcriptome analysis identified 223 homologs of Arabidopsis Ft genes in Chinese cabbage, and 50 of these genes responded to vernalization. RT-qPCR analysis of major Ft genes showed that the majority of flowering enhancers were up-regulated in response to vernalization, whereas most flowering repressors were down-regulated in response to vernalization. Among the major Ft genes, the expression of BrCOL1-2, BrFT1/2, BrSOC1/2/3, BrFLC1/2/3/5, and BrMAF was strongly affected by vernalization.

2018-11-02 | GSE106444 | GEO

Transcriptome Analysis Between Green Cabbage (Brassica oleracea var. capitata) and Savoy Cabbage (Brassica oleracea var. sabauda)

Project description:We found several candidate genes might be involved in the crinkled leaf phenotype of savoy cabbage.

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RNA-seqencing datasets for three different vernalization time course of radish

Project description:We report here NGS RNA-seqencing datasets for htree different vernalization time course of radish cultivar, "Taebaek".

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Transcriptome Analysis Between Green Cabbage (Brassica oleracea var. capitata) and Savoy Cabbage (Brassica oleracea var. sabauda)

Project description:Transcriptome Analysis Between Green Cabbage (Brassica oleracea var. capitata) and Savoy Cabbage (Brassica oleracea var. sabauda)

| PRJNA1030377 | ENA

High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves

Project description:Plant microRNAs are short (~21 nt), non-coding molecules that regulate gene expression by targeting mRNA cleavage or protein translation inhibition. In this manner, they play many important roles in the cells of living organisms. One of the plant species in which the entire set of miRNAs has not been yet completely identified is Brassica oleracea var. capitata (cabbage). For this reason and for the economic and nutritional importance of this food crop, Illumina high-throughput small RNAs sequencing has been performed to discover novel and conserved miRNAs in the mature cabbage leaves. In this study, raw reads generated from three small RNA libraries were bioinformatically processed and further analyzed to select sequences homologous to known B. oleracea and other plant miRNAs. As a result of this step, 267 conserved miRNAs (belonging to 62 families) have been discovered. The remaining unannotated tags were used in the prediction and evaluation of novel miRNAs, which resulted in the 26 potential miRNAs proposal. The expression of 13 selected miRNAs was analyzed by northern blot hybridization. To determine the functions and processes that these molecules may potentially regulate in cabbage leaves, GO annotation, GO enrichment analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapping of the predicted targets were performed. Taken together, for the first time, the large set of miRNAs was identified in the mature cabbage leaves. Potential target designation for these miRNAs may suggest their important role in the plant growth, development and other primary biological processes. The presented study not only supplements the knowledge about B. oleracea miRNAs, but also may be used in other researches concerning the improvement of the cabbage cultivation.

2014-06-13 | GSE45578 | GEO

Brassica oleracea-Alternaria brassicicola interaction during the early stages of leaf infection

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

Expression analysis of chinese cabbage (B.rapa ssp. pekinensis) : cold stress conditions

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2016-10-31 | GSE75145 | GEO

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