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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 mRNA]

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

PROVIDER: PRJNA720626 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14183382_1.fastq.gz	Fastqsanger.gz
	SRR14183382_2.fastq.gz	Fastqsanger.gz
	SRR14183383_1.fastq.gz	Fastqsanger.gz
	SRR14183383_2.fastq.gz	Fastqsanger.gz
	SRR14183384_1.fastq.gz	Fastqsanger.gz

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Project description:Background: The growth and development of leaf and petiole have an important influence on the photosynthesis of plants. The research on molecular mechanism of leaf and petiole development is of great significance, whether it is to improve plant photosynthetic efficiency, cultivate varieties with high photosynthetic efficiency, or improve the yield of crops using leaves as food organs. In this study, we aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). These data were then used to construct competitive endogenous RNA (ceRNA) networks, which can provide valuable information for better understanding the mechanism of leaf and petiole development. Results: In this study, the leaf and petiole of the baby Chinese cabbage inbred line ‘PHL’ were used as research materials for whole-transcriptome sequencing. A total of 10646 differentially expressed (DE) mRNAs, 303 DE lncRNAs, 7 DE circRNAs, and 195 DE miRNAs were identified between the leaf and petiole. Some transcription factors or proteins that play important roles in leaf and petiole development were identified, such as xyloglucan endotransglucosylase/hydrolase (XTH) protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, cellulose synthase (CESA), MOR1-like protein, and plant hormone biosynthesis related genes. Additionally, we constructed a leaf and petiole development-related ceRNA regulatory network, and obtained 85 pairs of ceRNA relationships, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA and 2 DEmiRNA-DEcircRNA. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaf and petiole of baby Chinese cabbage were screened from transcriptome data for subcellular localization analysis and overexpression transgenic verification. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoprotein and BrLSH2 has an obvious inhibitory effect on the growth and development of Arabidopsis thaliana. Conclusions: Our results revealed the potential mRNAs and non-coding RNAs (ncRNAs) involved in leaf and petiole development, which laid a foundation for further research on the molecular mechanism of leaf and petiole development in Chinese cabbage.

Dataset Information

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

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