TPGAS: The Transcriptome Platform for Gene Expression and Alternative Splicing Studies in Pepper (Capsicum annuum L.)

Hot pepper (Capsicum annuum) is one of the most consumed vegetable crops in the world and useful to human as it has many nutritional and medicinal values. Genomic resources of pepper are publically available since the pepper genome project had been completed. Nevertheless, only few transcriptomic resources are available for pepper. Here, we report the transcriptome platform for gene expression and alternative splicing (TPGAS) in pepper. A total of 147.35 Gb RNA-seq reads were generated from libraries containing five different tissues (stem, root, leaf, pericarp and placenta) and leaves infected by four pathogens of Capsicum annuum cv. CM334. By considering the gene structure of the pepper genome, the transcriptome was assembled into 162,908 transcripts and its total size was 318.88 Mb. To structurally annotate and construct accurate UniGene transcripts, we performed integrative gene annotation using reference proteins and ab initio method. For further works, the UniGene set will be used for analyzing 1) gene expression pattern to detect candidate transcripts that were expressed in specific tissue or pathogen infection and 2) alternative splicing event to identify splicing patterns and major transcript in each gene. In conclusion, TPGAS will serve as a valuable resource for isolation of differentially expressed and alternatively spliced genes in Capsicum annuum.