A fast and efficient protocol for small RNA extraction in Japanese plum and other Prunus species

Background: Small ribonucleic acids represent an important repertoire of mobile molecules that exert key roles in several cell processes including antiviral defense. Small RNA based repertoire includes both small interfering RNA (siRNA) and microRNA (miRNA) molecules. In the Prunus genus, sharka disease, caused by the Plum pox virus (PPV), first occurred on European plum (Prunus domestica) and then spread over among all species in this genus and thus classified as quarantine pathogen. Next-generation sequencing (NGS) was used for the study of siRNA/miRNA molecules; however, NGS relies on adequate extraction protocols. Currently, knowledge of PPV-Prunus interactions in terms of siRNA populations and miRNA species is still scarce, and siRNA/miRNA extraction protocols are limited to species such as peach, almond, and sweet cherry. Results: We describe a reliable procedure for siRNA/miRNA purification from Prunus salicina trees, in which previously used protocols did not allow adequate purification. The procedure was based on a combination of commercially available RNA purification kits and specific steps that yielded high quality purifications. The resulting molecules were adequate for library construction and NGS, leading to the development of a pipeline for analysis of both siRNAs and miRNAs in the PPV­P. salicina interactions. Results showed that PPV infection led to altered siRNA profiles in Japanese plum as characterized by decreased 24-nt and increased 21- and 22-nt siRNAs. Infections showed miR164 and miR160 generation and increased miR166, miR171, miR168, miR319, miR157, and miR159. Conclusion: We propose this protocol as a reliable and reproducible small RNA isolation procedure for P. salicina and other Prunus species.

Production of phenolic metabolites by Deschampsia antarctica shoots using UV-B treatments during cultivation in a photobioreactor

Deschampsia antarctica (DA), the only species in the Gramineae family endemic to the Antarctic territory, is characterized by a combination of high levels of free endogenous phenylpropanoid compounds under normal in situ and in vitro growth conditions. In this article, we describe the design and use of a specific temporary immersion photobioreactor to produce both increased DA biomass and secondary metabolite accumulation by UV-B elicitation during cultivation. Three min-long immersions in an induction medium applied every 4 hrs at 14ºC +/- 1 and 20/4 hrs light/darkness photoperiod increased DA biomass production over previous in vitro reports. Biomass duplication was obtained at day 10.7 of culturing, and maximum total phenolics and antioxidant activity were observed after 14 day of culturing. The addition of UV-B radiation pulses for 0.5 hrs at 6 hrs intervals increased total phenolics and antioxidant activity more than 3- and 1.5- fold, respectively, compared to controls with no UV-B. Significant accumulation of scopoletin, chlorogenic acid, gallic acid and rutin was found in these plantlets. This is the first bioreactor designed to optimize biomass and phenylpropanoid production in DA.