A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development

RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: Salsa. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.

Automated summary

A methodology was developed to transform RNA-Seq data from time course experiments into standardized expression profiles, facilitating analysis of gene expression changes during chili pepper fruit development. The developed R package Salsa provides researchers with valuable tools and insights for studying fruit development in chili peppers and other angiosperms.