Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

Abstract

Background Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively. Results These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development. Conclusions This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.

Small RNA profiling reveals the involvement of microRNA-mediated gene regulation in response to symbiosis in raspberry

“…Under drought stress, plants can effectively resist and adapt to drought stress by increasing root growth, changing root morphological structures, and reducing the damage to plants caused by drought stress ( Peng et al, 2013 ). miR396 targets mRNA coding for growth-regulating factor (GRF) transcription factors, rhodenase-like protein, and kinesin-like protein B ( Kong et al, 2022 ). Some members of the miR482 family can produce secondary siRNAs through targeted cleavage of nucleotide binding site-leucine rich repeat-like (NBS-LRR-like) genes, thereby silencing and regulating a variety of genes related to plant disease resistance, including NBS-LRR-like genes ( Sagi et al, 2017 ).…”

Identifying long non-coding RNAs involved in heat stress response during wheat pollen development

“…For example, sufficient expression of lncRNA LONG-DAY–SPECIFIC MALE-FERTILITY–ASSOCIATED RNA or in short, LDMAR is essential for pollen development and fertility in rice; even a single nucleotide mutation alters the secondary structure and expression of LDMAR, which leads to photoperiod-sensitive male sterility ( Ding et al., 2012 ). Previously, the differential and specifical expression of several lncRNAs during pollen developmental stages has been reported in plants such as Brassica rapa ( Huang et al., 2018 ; Lohani et al., 2023 ), Camellia oleifera ( Kong et al., 2022 ), and Oryza sativa ( Wang et al., 2021 ). During pollen development, lncRNAs can also be differently expressed in response to environmental challenges, which points to the regulatory role of lncRNAs as stress-responsive molecules.…”