Identification and analysis of small RNAs in exosome-like nanoparticles derived from onion (Allium cepa L.)

Small RNAs (sRNAs) in plant-derived exosome-like nanoparticles (PELNs) have attracted considerable attention as biologically active substances that play a crucial role in cross-kingdom regulatory processes. However, there is insufficient research dedicated to identifying sRNAs within PELNs. We aimed to analyze the expression profile of sRNAs in onion-derived exosomes-like nanoparticles (OELNs) and explore their potential role in cross-kingdom regulation. In this study, OELNs were extracted, possessing an optimal particle size of approximately 139 nm and a Zeta potential of roughly -20 mV. Subsequently, high-throughput small RNA sequencing was conducted to analyze sRNAs in onion tissues and OELNs. The expression profile of sRNAs in OELNs was elucidated, and it was predicted that highly expressed microRNAs (miRNAs) in OELNs may exert potential regulatory effects on the human genome. By comparing with the reference genome of onion (Allium cepa L.), 11 known miRNAs and 248 novel miRNAs were identified in both onion tissues and OELNs. Target gene prediction analysis of the human genome has revealed that 20 miRNAs highly expressed in OELNs potentially participate in the regulation of human tumor and cardiovascular-related signaling pathways. Furthermore, differential analysis was conducted on small/short interfering RNA (siRNA), small nucleolar RNA (snoRNA), and transfer ribonucleic acid (tRNA) in OELNs. This study laid a theoretical foundation for further exploring the cross-kingdom role of non-coding RNAs in OELNs, and provided new ideas for the development of plant-derived functional components.