Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

Fengyan Shi,Chuanhong Liu,Hui Feng,Xueling Ye,Jie Ren,Zhiyong Liu,Chong Tan,Li Zhou,Zhijin Pang

doi:10.1038/s41598-022-06556-2

Fengyan Shi, Chuanhong Liu + Show 7 more

Open Access

https://doi.org/10.1038/s41598-022-06556-2

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Abstract

Anther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestris L. ssp. pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA–DEmRNA, 281 DEmiRNA–DElncRNA, and 23 DEmiRNA–DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers of Arabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.

Highlights

In recent years, with the rapid development of high-throughput sequencing technology, genome-wide differential RNA expression analysis has allowed whole-transcriptome level studies on anther development in flowering plants[13,14]
Two novel miRNAs that are expressed in flower buds were identified in Chinese cabbage, and their targeted sucrose transporters, SUC1 and H(+)-ATPase 6, were found to be inhibited, possibly leading to an energy deficiency and pollen abortion16. long non-coding RNAs (lncRNAs) is a type of ncRNA, exceeding 200 nt in length, and mainly transcribed from the antisense chain and spacer region of the protein-coding gene. lncRNAs are involved in many important regulatory processes such as genomic imprinting, chromatin modification, transcriptional activation, transcriptional interference, and nuclear transport[17,18]
Our results revealed that the regulatory network of competitive endogenous RNA (ceRNA)–miRNA–target genes may be involved in anther development in Chinese cabbage

Summary

Introduction

With the rapid development of high-throughput sequencing technology, genome-wide differential RNA expression analysis has allowed whole-transcriptome level studies on anther development in flowering plants[13,14]. Fan et al.[29] constructed a ceRNA network to elucidate the potential mechanism of Paulownia witches’ broom disease by analyzing the expression of miRNAs, lncRNAs, circRNAs, and mRNAs. In rice, a ceRNA network was constructed, which may play an important role in regulating the response of phosphate-starved p lants[30]. The regulatory network of ceRNA in the anther development of Chinese cabbage has not yet been established, and the interactions among circRNAs, lncRNAs, miRNAs, and mRNAs in anther development require further study. We performed whole-transcriptome sequencing of anthers samples (‘Ant’) and samples of the vegetative mass of four true leaves (‘Mix’), identified changes in the expression of miRNAs, lncRNAs, circRNAs, and mRNAs, and analyzed their potential regulatory roles using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) databases. A ceRNA network was established, which lays the foundation for exploring the potential regulatory mechanism of Chinese cabbage anther development

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