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Symplocarpus renifolius

ABSTRACT: Mechanism underlying sugar translocation and transport in Asian skunk cabbage.

PROVIDER: PRJDB15002 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR426690.fastq.gz	Fastqsanger.gz
	DRR426691.fastq.gz	Fastqsanger.gz
	DRR426692.fastq.gz	Fastqsanger.gz
	DRR426693.fastq.gz	Fastqsanger.gz
	DRR426694.fastq.gz	Fastqsanger.gz

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Symplocarpus renifolius

Project description:Gene expression analysis in floral tissues from thermogenic skunk cabbage

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SuperSAGE data from skunk cabbage spadices

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Project description:Developmentally regulated thermogenesis in the Asian skunk cabbage

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SuperSAGE data from skunk cabbage spadices

Project description:This study aims at investigating the gene expression profile of thermogenic skunk cabbage (Symplocarpus renifolius). Using Super-SAGE, we compared the gene expression profile of different developmental stages of skunk cabbage spadices. To obtain the SuperSAGE libraries, we followed the original SuperSAGE protocol described by Matsumura and colleagues (Matsumura et al., 2003) with some modification. Total RNA of spadices in different developmental stage (immature, female, bisexual, and male) were isolated using RNAiso reagent. The SuperSAGE library was directly sequenced with a large-scale pyrosequencing method.

2011-12-22 | E-GEOD-29852 | biostudies-arrayexpress

Loss of BraA09g066480.3C leads to a wax-less phenotype in flowering Chinese cabbage

Project description:PURPOSE:To clarify the mechanism of the wax deficiency, the wax-less flowering Chinese cabbage doubled-haploid (DH) line ‘CX001’ and Chinese cabbage DH line ‘FT’, obtained from isolated microspore culture, were used in the experiments. Transcriptome analysis indicated that BraA09g066480.3C was expressed in ‘FT’ but not in ‘CX001’.The work presented herein demonstrated that BraA09g066480.3C was the causal gene for wax-less flowering Chinese cabbage ‘CX001’

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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.

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Whole-transcriptome analysis and construction of ceRNA-miRNA-target gene regulatory networks in anther development of Chinese cabbage (Brassica campestris L. ssp. pekinensis) [Anther & mixed parts miRNA-seq]

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

Symplocarpus

Project description:phylogeography of genus Symplocarpus in Northeast Asia

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Scottish Vitamin D Intervention Study

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Project description:Transcriptome sequencing between swollen root of cabbage translocation line and normal root Chinese cabbage

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