Supplementary Tables v2

Pepper<i> </i>is an important spice and a model plant for fruit development studies. Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis. Here, we generated full-spectrum spatio-temporal transcriptome data of chili peppers eight tissues at five growth stages using the Oxford Nanopore long-read sequencing approach. We report the identification of 453,318 novel transcripts and provide an analysis of transcript diversity and splicing events. We also report five types of alternative splicing events. The number of expressed tissue-specific transcripts ranged from 177 (stem) to 6174 (seed). We discuss in detail the expression changes during fruit and placenta development. Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper selfing line 8214 is mainly derived from valine, leucin, and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways. The data generated in this study has been used to develop a user-friendly pepper full-length transcriptome variation database (http://pepper-database.cn/). It provides transcriptomics and genomics information and allows users to analyze the data using various tools implemented. Our work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology.