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

摘要

Intron retention is the most common alternative splicing event in plants and plays a crucial role in the responses of plants to environmental signals.Despite a large number of RNA-seq libraries from different treatments and genetic mutants stored in public domains,a resource for querying the intron-splicing ratio of individual intron is still required.Here,we established the first-ever large-scale splicing efficiency database in any organism.Our database includes over 57,000 plant public RNA-seq libraries,comprising 25,283 from Arabidopsis,17,789 from maize,10,710 from rice,and 3,974 from soybean,and covers a total of 1.6 million introns in these four species.In addition,we 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 various tissues,developmental stages,and stress-related conditions.The result is a large collection of 3,313treatment conditions and 3,594 genetic mutants for discovering differentially regulated splicing efficiency.Our online database can be accessed at https://plantintron.com/.