Study : Gene expression profiling study by RNA-seq for identifying genes associated with sound vibration in plant
Gene expression profiling study by RNA-seq for identifying genes associated with sound vibration in plant
Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed a gene expression profiling basd on RNA-seq experiment to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum. Overall design: A group of plants was prepared to be expose to sound vibration (SV, 10 kHz) at 90 dB every 3 h for 10 days. Another group of plants dreched with benzothiadiazole (BTH) were also prepared as a positive control group. The other group of plants with non-treatment were also prepared as a control group. Then, all samples were drenched with a pathogen (R. solanacearum). Transcriptome data were generated by performing RNA-seq analysis of 29 arabidopsis samples, which were obtained at 0d, 1d and 2d after dreching pathogen. Each sample group contains three biological replicates, except for a 10kHz sound wave treated group obtained at 1d after drenching pathogen (4 replicates) and a non-treatment group obtained at 2d after drenching pathogen (4 replicates). Total RNA was isolated from Arabidopsis roots using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The quality and integrity of total RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by a visual examination of RNA under ultraviolet light. RNA-seq library was prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) and sequenced on the Illumina Hiseq2500 platform to generate 100 bp paired-end reads.