Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis

Setaria viridis (green foxtail millet) is a partially domesticated relative of the widely cultivated foxtail millet (S. italica) with significant potential as a crop in its own right. Here we focus on the transcription of repetitive elements in S. viridis in different transcriptome fractions, using both Ribo-depleted and Poly-A libraries. For RNA analysis, Setaria viridis cv.A10 seeds were washed with distilled water and sterilized by incubating in a solution of 20% sodium hypochlorite and 0,1% of Tween 20. Seed were germinated in petri dishes in MS medium for 5 days, followed by 7 days in plastic pots. After root system establishment, the seedling were transferred to pots containing a mixture of substrate and sand (1:1) and grown in a plant chamber in under a photoperiod of 16/8h (light/dark), temperature of 25 degrees for at least 20 days. RNA of leaf was extracted with RNeasy Plant mini kit and libraries were prepared by using NEB kit E6440S. Sequencing of the libraries (Ribo-depleted and Poly-A in triplicates) were performed by using Illumina Novaseq 6000 (Genomic Centre, Queen Mary University of London), generating 150 bp paired-end reads. Transcriptomes were sequenced and compared for differential proportion of transposable elements.