Plant Intron Splicing Efficiency Database (PISE): exploring splicing of ~1,650,000 introns in Arabidopsis, maize, rice and soybean from ~57,000 public RNA-seq libraries

Abstract

Intron retention is the most common form of alternative splicing events in plants and plays a crucial role in plants responding to environmental signals. Despite a large number of RNA-seq libraries from different treatments and genetic mutants stored at public domains, a resource for querying the intron splicing ratio of individual introns is still missing. Here, we established the first-ever large-scale splicing efficiency database to date in any organism. Our database includes more than 57,000 plant public RNA-seq libraries, including 25,283 from Arabidopsis, 17,789 from maize, 10,710 from rice, and 3,974 from soybean, and in total covers more than 1.6 million introns in these four species. In addition, we have manually curated and annotated all the mutant-and treatment-related libraries as well as their matched controls included in our library collection, and added graphics to display intron splicing efficiency across different tissues, developmental stages, and stress-related conditions. The result is a large collection of 3,313 treatment conditions and 3,594 genetic mutants for discovering the differentially regulated splicing efficiency. Our online database can be accessed at https://plantintron.com/.