Journal
PLANT JOURNAL
Volume 91, Issue 3, Pages 518-533Publisher
WILEY
DOI: 10.1111/tpj.13571
Keywords
abscisic acid; alternative splicing; Arabidopsis thaliana; proteogenomics; splicing factor; translation; technical advance
Categories
Funding
- Natural Science Foundation of Shandong Province [BS2015NY002]
- National Natural Science Foundation of China [NSFC31301251, NSFC31101099]
- Science and Technology Programme of Nantong [MS12016044]
- Training Programme for University Prominent Young and Middle-aged Teachers and Presidents
- National Basic Research Programme of China [2012CB114300]
- JSPS 'Strategic Young Researcher Overseas Visits Programme for Accelerating Brain Circulation' [S2503]
- Shenzhen Overseas Talents Innovation and Entrepreneurship Funding Scheme (The Peacock Scheme) [KQTD201101]
- Hong Kong Research Grant Council [AoE/M-05/12, CUHK 14122415, CUHK 14160516]
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In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.
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