Transcriptomics,Genomics

Dataset Information

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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]


ABSTRACT: 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. 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.

INSTRUMENT(S): Illumina HiSeq 2500 (Brassica rapa subsp. pekinensis)

ORGANISM(S): Brassica rapa subsp. pekinensis  

SUBMITTER: Zhiyong Liu  

PROVIDER: GSE171708 | GEO | 2021-11-17

REPOSITORIES: GEO

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GSE171708_All_Expressed_miRNA.txt.gz Txt
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Publications

Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis).

Shi Fengyan F   Xu Hezi H   Liu Chuanhong C   Tan Chong C   Ren Jie J   Ye Xueling X   Feng Hui H   Liu Zhiyong Z  

BMC genomics 20211113 1


<h4>Background</h4>The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenou  ...[more]

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