Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction

Genome-wide identification of long non-coding RNAs reveals potential association with Phytophthora infestans asexual and sexual development

Long non-coding RNAs (lncRNAs) play pivotal roles in regulating diverse biological processes across plants, mammals, and fungi. However, the information on lncRNAs in oomycete asexual and sexual reproduction, which are two pivotal processes in the pathogenic cycle, has not been elucidated. In this present study, strand-specific RNA sequencing data of Phytophthora infestans with asexual development and sexual reproduction were reanalyzed, and a total of 4,399 lncRNAs were systematically identified. Compared to messenger RNAs (mRNAs), lncRNAs had a higher proportion of transcripts containing more than one exon, shorter nucleotide lengths, and lower expression levels. Target analysis showed that although only 280 lncRNA-mRNA pairs were shared, the functional pathways in which cis and trans targets participated were similar. Weighted gene co-expression network analysis of differentially expressed lncRNAs (DElncRs) and differentially expressed mRNAs (DEmRs) of asexual development stages indicated that lncRNAs might participate in different asexual stages and transformation of the growth stages via regulating functional genes. Expression trend analysis of DElncRs and DEmRs showed that lncRNAs may promote asexual development via upregulating mRNAs encoding development- and invasion-related proteins, such as INF6, triosephosphate isomerase, and glycoprotein elicitor. Co-expression analysis of DElncRs and DEmRs of sexual reproduction showed that lncRNAs could increase the level of mRNAs related to mating, such as M96 mating-specific protein and Crinkler family protein, which meant that lncRNAs might participate in sexual reproduction by regulating mating-related genes. Our study conducted a comprehensive analysis of lncRNAs in P. infestans and suggested a potential function of lncRNAs in asexual and sexual development.

IMPORTANCE

This study systematically analyzed lncRNAs in Phytophthora infestans, revealing the associations between lncRNAs and functional genes. The potential regulatory roles of lncRNAs in the asexual and sexual reproduction stages were clarified, providing a new perspective for in-depth understanding of the reproductive regulatory network of oomycetes. This not only expands the understanding of the functions of non-coding RNAs in different biological groups but also provides potential targets for the development of new disease prevention and control strategies, promoting related research in the fields of agriculture and biology.

MicroRNAs in Plants Development and Stress Resistance

Plant growth and development are governed by a rigorously timed sequence of ontogenetic programmes. MicroRNAs (miRNAs), a class of short noncoding RNAs, function as master regulators of gene expression by targeting mRNAs for cleavage or direct translational inhibition at the posttranscriptional level in eukaryotes. Numerous miRNA molecules that control significant agronomic properties in plants have been found. On the one hand, miRNAs target transcription factors (TFs) to determine plant structure, such as root development, internode elongation, leaf morphogenesis, sex determination and nutrient transition. On the other hand, miRNAs alter expression levels to adapt to biological and abiotic stresses, including fungi, bacteria, viruses, drought, waterlogging, high temperature, low temperature, salinity, nutrient deficiencies, heavy metals and other abiotic stresses. To fully understand the role of miRNAs in plants, we review the regulatory role of miRNAs in plant development and stress resistance. Beyond that, we propose that the novel miRNA in review can be effectively further studied with artificial miRNA (amiRNA) or short tandem target mimics (STTM) and miRNA delivery in vitro can be used to improve crop yield and agricultural sustainability.

microRNAs: Key Regulators in Plant Responses to Abiotic and Biotic Stresses via Endogenous and Cross-Kingdom Mechanisms

Dramatic shifts in global climate have intensified abiotic and biotic stress faced by plants. Plant microRNAs (miRNAs)-20-24 nucleotide non-coding RNA molecules-form a key regulatory system of plant gene expression; playing crucial roles in plant growth; development; and defense against abiotic and biotic stress. Moreover, they participate in cross-kingdom communication. This communication encompasses interactions with other plants, microorganisms, and insect species, collectively exerting a profound influence on the agronomic traits of crops. This article comprehensively reviews the biosynthesis of plant miRNAs and explores their impact on plant growth, development, and stress resistance through endogenous, non-transboundary mechanisms. Furthermore, this review delves into the cross-kingdom regulatory effects of plant miRNAs on plants, microorganisms, and pests. It proceeds to specifically discuss the design and modification strategies for artificial miRNAs (amiRNAs), as well as the protection and transport of miRNAs by exosome-like nanovesicles (ELNVs), expanding the potential applications of plant miRNAs in crop breeding. Finally, the current limitations associated with harnessing plant miRNAs are addressed, and the utilization of synthetic biology is proposed to facilitate the heterologous expression and large-scale production of miRNAs. This novel approach suggests a plant-based solution to address future biosafety concerns in agriculture.