A CTAB protocol for obtaining high-quality total RNA from cinnamon (Cinnamomum zeylanicum Blume).

Cinnamomum zeylanicum Blume is an endemic Sri Lankan species commonly known as Ceylon cinnamon or true cinnamon. It is considered the king of spices in addition to its medicinal benefits. Despite recent scientific evidence on its medicinal properties and the industrial demand, cinnamon breeding and crop improvement are not been improved to the expectation. It is mainly due to the limited availability of the genomic information of cinnamon, linked with technical challenges caused by abundant secondary metabolites in all plant parts. Therefore, obtaining high-quality RNA is the fundamental step of transcriptomic analysis and the gene discovery process of cinnamon. We have optimized a CTAB based protocol for high-quality RNA extraction from different cinnamon tissues at various maturity stages collected from the field. Regular pH around 8 and the presence of Polyvinylpyrrolidone (PVP) in CTAB buffer increased the viscosity of the cinnamon lysate. Adjusting the pH of the lysis buffer to 6-6.5 reduced the viscosity of lysate while chloroform precipitates protein efficiently at the adjusted pH with no phenol. Therefore, this protocol excludes PVP and phenol extraction steps. Nanodrop spectrophotometer, gel electrophoresis, and bioanalyzer readings confirmed the quality of extracted RNA. RNA-seq libraries prepared were sequenced with Illumina Sequencing by synthesis technology and obtained good quality data to be used for transcriptomic analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02756-1. © King Abdulaziz City for Science and Technology 2021.