RNA-seq analysis to investigate transcripts in different pAMT alleles

putative aminotransferase (pAMT) is an essential gene in capsaicinoid biosynthesis in chili pepper fruits. A series of studies have demonstrated that loss-of-function of pAMT caused a drastic reduction in capsaicinoid content. pAMT encodes an aminotransferase, which produces vanillylamine, a precursor of capsaicinoids, from vanillin. In this project, we found two mutant alleles of pAMT (pamtL1 and pamtL2), which harbor a Tcc transposon in different positions in intron 3. Both alleles exhibited leaky pAMT activities, but pamtL2 had a more severe negative effect on capsaicinoid content. The RNA-seq analysis aimed to demonstrate how intronic transposon affect transcription and splicing process in pAMT. RNA-seq data were obtained from placental tissue in four different accessions