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| Status |
Public on Nov 17, 2021 |
| Title |
Whole-transcriptome analysis and construction of vernalization-related ceRNA-miRNA-target gene regulatory network in Chinese cabbage (Brassica campestris L. ssp. pekinensis) [seed mRNA] |
| Organism |
Brassica rapa subsp. pekinensis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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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| Overall design |
we performed the whole-transcriptome sequencing on Chinese cabbage seeds that were vernalized at 4℃ for 25 days and seeds that were not vernalized, identified the expression changes of mRNA, miRNA, lncRNA, and circRNA, and carried out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichment analysis to explore their potential regulatory role.
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| Contributor(s) |
Liu Z, Shi F, Xu H |
| Citation(s) |
34773977 |
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| Submission date |
Apr 08, 2021 |
| Last update date |
Nov 17, 2021 |
| Contact name |
Zhiyong Liu |
| E-mail(s) |
tanchong123@syau.edu.cn
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| Organization name |
Shenyang Agriculral University
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| Street address |
Dongling Road 120
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| City |
Shenyang |
| State/province |
Liaoning Province |
| ZIP/Postal code |
110866 |
| Country |
China |
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| Platforms (1) |
| GPL29989 |
Illumina NovaSeq 6000 (Brassica rapa subsp. pekinensis) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA720626 |
| SRA |
SRP314016 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE171707_circRNA_expression.txt.gz |
72.0 Kb |
(ftp)(http) |
TXT |
| GSE171707_linear_isoforms_expression.txt.gz |
5.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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