Whole transcriptome profiling of zhongyan90

Cytoplasmic male sterility (CMS) is of great significance in breeding, but few investigations have been conducted to explore the CMS fertility mechanisms in crops based on the whole transcriptome and its ceRNA network. To systematically understand the molecular mechanism of CMS, the whole transcriptomes of the flower buds from both CMS line and maintainer line of tobacco cultivar zhongyan90 were sequenced and analyzed in this manuscript, and a total of 2,247 differentially expressed mRNAs (DEmRNAs), 529 DElncRNAs, 59 DEmiRNAs and 16 DEcircRNAs were identified, of which all but DElncRNAs were predominantly expressed in the down-regulated pattern, and these DERNAs were mainly involved in the important physiological activities such as signal transduction, enzymatic reactions and metabolic processes. Analyses of the CMS-related ceRNA regulatory network further suggested that the plant hormone signal transduction pathway might play a particularly important role in tobacco CMS; ten CMS candidate genes probably had key functions in tobacco flower development, which matched with our anther morphology observations and literature evidences; three DElncRNAs and one DEcircRNA potentially regulated CMS candidate gene expression through the mediation of miR156 and miR172, and some of these miRNAs could even be participated in nucleoplasmic signaling; and the newly identified miR6164 family possibly also contributesd an important, but as yet unrevealed effect in regulating tobacco CMS. The subsequent qRT-PCR validation results on important CMS candidate genes conclusively confirmed the reliability of the RNA-seq data and the down-regulation of the expression in CMS line. Our findings will strengthen the foundation for exploring the molecular mechanisms of tobacco CMS from whole transcriptome perspectives, and provide novel ideas for genetic improvement and hybrid advantage utilization in related crops