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| Status |
Public on Dec 29, 2022 |
| Title |
Whole-transcriptome analysis and construction of a leaf and petiole development-related ceRNA regulatory network in baby Chinese cabbage (Brassica campestris L. ssp. pekinensis) |
| Organism |
Brassica rapa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
In this study, whole-transcriptome sequencing was performed on leaf and petiole samples of baby Chinese cabbage. A total of 10646 DEmRNAs, 303 DElncRNAs, 7 DEcircRNAs, and 195 DEmiRNAs were identified as being differentially expressed between ‘leaf’ and ‘pet’. GO annotation and KEGG pathway enrichment analyses were performed on the differentially expressed RNAs, revealing their important roles in the regulation of leaf and petiole development. Some transcription factors and proteins that play important roles in leaf and petiole development were identified, such as XTH protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, CESA, MOR1-like protein, and plant hormone biosynthesis related genes. Moreover, we constructed the first leaf and petiole development-related ceRNA‒miRNA–target gene regulatory network in Chinese cabbage, comprising 41 DEmRNAs, 18 DEmiRNAs, 9 DElncRNAs, and 1 DEcircRNAs. The subcellular localization analysis and over expression transgenic verification of BrLSH1, BrLSH2 and BrLSH3, which were differentially expressed between the leaf and petiole, were carried out. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoproteins, and BrLSH2 significantly inhibited the growth and development of Arabidopsis thaliana. Our findings provide a systematic recognition of mRNA and ncRNA related to leaf and petiole development, and lay a foundation for further exploring the molecular regulation mechanism of leaf and petiole development in Chinese cabbage.
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| Contributor(s) |
Liu Z, Shi F, Zhao Z, Jiang Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Nov 29, 2022 |
| Last update date |
Dec 30, 2022 |
| Contact name |
jun zhang |
| E-mail(s) |
jzhang@lc-bio.com
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| Organization name |
Shenyang Agricultural University
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| Street address |
liaoning
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| City |
shenyang |
| ZIP/Postal code |
110000 |
| Country |
China |
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| Platforms (1) |
| GPL28300 |
Illumina NovaSeq 6000 (Brassica rapa) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA906453 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE218959_genes_fpkm_expression.txt.gz |
5.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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