Abstract
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 3,313 treatment conditions and 3,594 genetic mutants for discovering differentially regulated splicing efficiency. Our online database can be accessed at https://plantintron.com/.
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Acknowledgements
We thank all the research groups that contributed RNA-seq data to the community, and we regret not being able to cite all the related papers in the main text owing to space constraints. References for all libraries used are listed in PISE ‘All Libraries’. Computation was supported by Center for Computational Science and Engineering at Southern University of Science and Technology. The group of J.Z. was 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), and the Stable Support Plan Program of Shenzhen Natural Science Fund (20200925153345004). J.J. was supported by the National Natural Science Foundation of China (32100444) and the Shenzhen Fundamental Research Program (JCYJ20210324105202007).
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Zhang, H., Jia, J. & Zhai, J. 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. Sci. China Life Sci. 66, 602–611 (2023). https://doi.org/10.1007/s11427-022-2193-3
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DOI: https://doi.org/10.1007/s11427-022-2193-3