De novo assembly transcriptome in chili pepper

To understand more knowledge in biosynthesis of capsaicinoids, we performed RNA-seq of the placenta and pericarp of pungent pepper (Capsicum frutescens L.) using the de novo assembly. We obtained a total 75,536 high-quality transcripts using Trinity software. About 71.57% of unigenes showed similarity to the public protein sequences (60.55%) and genome of potato and tomato (65.70%). Our result predicted 3 new structure genes, which filled gaps of the pathway of capsaicinoid biosynthesis and revealed new candidate genes involve in capsaicinoid biosynthesis based on KEGG analysis. A significant number of SSR and SNPs markers were predicted in Capsicum frutescens sequences, which will be helpful to the identification of polymorphisms within chili pepper populations. These data will provide new clue to the pathway of capsaicinoid biosynthesis and biology of chili pepper. In addition, our strategy of de novo assembly transcriptome can helpful to other similar studies.