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  

作　　者：Hong Zhang Jinbu Jia Jixian Zhai 

机构地区：[1]Department of Biology,School of Life Sciences,Southern University of Science and Technology,Shenzhen 518055,China [2]Institute of Plant and Food Science,Southern University of Science and Technology,Shenzhen 518055,China [3]Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes,Institute of Plant and Food Science,Department of Biology,Southern University of Science and Technology,Shenzhen 518055,China

出　　处：《Science China(Life Sciences)》2023年第3期602-611,共10页中国科学（生命科学英文版）

基　　金：supported by the National Key R&D Program of China(2019YFA0903903);the Program for Guangdong Introducing Innovative and Entrepreneurial Teams(2016ZT06S172);the Shenzhen Sci-Tech Fund(KYTDPT20181011104005);the Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes(2019KSYS006);the Stable Support Plan Program of Shenzhen Natural Science Fund(20200925153345004);supported by the National Natural Science Foundation of China(32100444);the Shenzhen Fundamental Research Program(JCYJ20210324105202007)。

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/.

关 键 词：SPLICING RNA-SEQ PLANT DATABASE 

分 类 号：S513[农业科学—作物学]