Chapter 15 Infographic: Overview scheme of transcriptomics in plants with emphasis on the RNA-seq method. (a) Sample preparation and RNA isolation. (b) Library preparation starts by selecting the RNA species from the total RNA, followed by fragmentation of the RNA sequence, cDNA synthesis, adapter ligation, cDNA amplification, and RNA sequencing. (c) The first step in transcriptome analysis is assessing the quality and quantity of reads. The clean reads are assembled to the reference genome or through a de-novo assembly or by combining these two approaches. The assemble reads are then annotated, followed by quantification and normalisation of the annotated results. The final step is differential expression analysis to quantify the difference in the expression level of genes between the samples or treatments.