Whole transcriptome analysis of leaves and petioles in Chinese cabbage
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ABSTRACT:
PROVIDER: PRJNA755858 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15508084_1.fastq.gz | Fastqsanger.gz | |||
| SRR15508084_2.fastq.gz | Fastqsanger.gz | |||
| SRR15508085_1.fastq.gz | Fastqsanger.gz | |||
| SRR15508085_2.fastq.gz | Fastqsanger.gz | |||
| SRR15508086_1.fastq.gz | Fastqsanger.gz |
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Project description:Whole transcriptome analysis of leaves and petioles in Chinese cabbage [miRNA]
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Project description:Whole transcriptome analysis of leaves and petioles in Chinese cabbage [circRNA]
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Project description:Using 300K′-high density microarray covering the chinese cabbage whole genome, genome-wide expression analyses of cold stress conditions.
2016-10-31 | GSE75145 | GEO
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 | GSE171707 | GEO
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
Project description:Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. A total of 9055 mRNA, 585 miRNA, 1344 lncRNA, and 165 circRNA were identified as differentially expressed in the anther of Chinese cabbage compared with Mix (roots, stems and leaves) by whole-transcriptome sequencing. The anther-related ceRNA-miRNA-target gene regulatory network through miRNA targeting relationships was constructed and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions were obtained in Chinese cabbage. The genes in the ceRNA network were enriched in the pathways including starch and sucrose metabolism, carbon metabolism, pyruvate metabolism and carbon fixation in photosynthetic organisms, plant hormone signal transduction, and RNA degradation. This study identified some important genes and their interaction lncRNAs, circRNAs, and miRNAs involved in microsporogenesis (BraA06g035480.3C), tapetum and callose layer development (BraA09g009280.3C, BraA04g028920.3C, and BraA10g022680.3C etc), pollen wall formation (BraA06g000980.3C, BraA02g023130.3C, and BraA10g029650.3C etc), and anther dehiscence (BraA10g027200.3C, BraA04g023740.3C, and BraA04g030860.3C etc). Additionally, we analyzed the promoter activity of six anther predominant expression genes, and the results showed that they were all expressed specifically in the anther of Chinese cabbage. This study lay the foundation for further research on the molecular mechanism of anther growth and development.
2022-02-23 | GSE171705 | GEO
Project description:Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. A total of 9055 mRNA, 585 miRNA, 1344 lncRNA, and 165 circRNA were identified as differentially expressed in the anther of Chinese cabbage compared with Mix (roots, stems and leaves) by whole-transcriptome sequencing. The anther-related ceRNA-miRNA-target gene regulatory network through miRNA targeting relationships was constructed and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions were obtained in Chinese cabbage. The genes in the ceRNA network were enriched in the pathways including starch and sucrose metabolism, carbon metabolism, pyruvate metabolism and carbon fixation in photosynthetic organisms, plant hormone signal transduction, and RNA degradation. This study identified some important genes and their interaction lncRNAs, circRNAs, and miRNAs involved in microsporogenesis (BraA06g035480.3C), tapetum and callose layer development (BraA09g009280.3C, BraA04g028920.3C, and BraA10g022680.3C etc), pollen wall formation (BraA06g000980.3C, BraA02g023130.3C, and BraA10g029650.3C etc), and anther dehiscence (BraA10g027200.3C, BraA04g023740.3C, and BraA04g030860.3C etc). Additionally, we analyzed the promoter activity of six anther predominant expression genes, and the results showed that they were all expressed specifically in the anther of Chinese cabbage. This study lay the foundation for further research on the molecular mechanism of anther growth and development.
2022-02-23 | GSE171706 | GEO
Project description:The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line âFTâ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line âFTâ, the drmâs chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between âFTâ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between âFTâ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage. The RNA from the third true leaves (day 15 to day 24 after the appearance of the third true leaves) of a developmentally retarded mutant (drm) and its wild type âFTâ in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
2016-03-01 | E-GEOD-75464 | biostudies-arrayexpress
Project description:We use Chinese cabbage PHL as the material and sample during maturing repeating three times. 44796 differentially expressed mRNAs were identified by complete transcriptome sequencing of leaf and petiole, of which 10646 were significant differentially expressed. There were 10422 significant differentially expressed mRNAs annotated into molecular function, biological process and cell components. There were 723 GO terms, and the most enriched GO term was membrane component (GO: 0016021) . KEGG analysis showed that there were 31 significant pathways. Among them, the plant hormone signal transduction pathway (Ko04075) is the pathway with the most differentially enriched genes.A total of 2553 differentially expressed lncRNAs were obtained, of which 303 were significant differentially expressed lncRNAs. Target genes of significantly differentially expressed lncRNAs were predicted, and the predicted target genes were analyzed by GO and KEGG. There were 2425 GO terms and 127 pathways. The most enriched GO term was nucleus (GO: 0005634) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 1070 differentially expressed miRNAs were obtained, of which 195 were significant differentially expressed. Go and KEGG analyses of the predicted target genes were performed. There were 551 GO terms and 24 pathways. The most abundant GO terms were membrane components (GO: 0016021) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 886 differentially expressed circRNAs were obtained, including 7 significant differentially expressed circRNAs, which have 3 up-regulated circRNAs and 4 down-regulated circRNAs.
2022-08-26 | GSE182326 | GEO
Project description:We use Chinese cabbage PHL as the material and sample during maturing repeating three times. 44796 differentially expressed mRNAs were identified by complete transcriptome sequencing of leaf and petiole, of which 10646 were significant differentially expressed. There were 10422 significant differentially expressed mRNAs annotated into molecular function, biological process and cell components. There were 723 GO terms, and the most enriched GO term was membrane component (GO: 0016021) . KEGG analysis showed that there were 31 significant pathways. Among them, the plant hormone signal transduction pathway (Ko04075) is the pathway with the most differentially enriched genes.A total of 2553 differentially expressed lncRNAs were obtained, of which 303 were significant differentially expressed lncRNAs. Target genes of significantly differentially expressed lncRNAs were predicted, and the predicted target genes were analyzed by GO and KEGG. There were 2425 GO terms and 127 pathways. The most enriched GO term was nucleus (GO: 0005634) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 1070 differentially expressed miRNAs were obtained, of which 195 were significant differentially expressed. Go and KEGG analyses of the predicted target genes were performed. There were 551 GO terms and 24 pathways. The most abundant GO terms were membrane components (GO: 0016021) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 886 differentially expressed circRNAs were obtained, including 7 significant differentially expressed circRNAs, which have 3 up-regulated circRNAs and 4 down-regulated circRNAs.
2022-08-26 | GSE182325 | GEO