Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

• DOI: 10.1111/tpj.13571
• Publication Date: 2017-04-13T16:10:26Z
• Authors: Fu‐Yuan Zhu; Mo‐Xian Chen; Neng‐Hui Ye; Lu Shi; Kai‐Long Ma; Jing‐Fang Yang; Yun‐Ying Cao; Youjun Zhang; Takuya Yoshida; Alisdair R. Fernie; Guang‐Yi Fan; Bo Wen; Ruo Zhou; Tie‐Yuan Liu; Tao Fan; Bei Gao; Di Zhang; Ge‐Fei Hao; Shi Xiao; Ying‐Gao Liu; Jianhua Zhang
• Keywords: Splicing factor

In eukaryotes, mechanisms such as alternative splicing (AS) and translation initiation (ATI) contribute to organismal protein diversity. Specifically, factors play crucial roles in responses environment development cues; however, the underlying are not well investigated plants. Here, we report parallel employment of short-read RNA sequencing, single molecule long-read sequencing proteomic identification unravel AS isoforms previously unannotated proteins response abscisic acid (ABA) treatment. Combining data from two methods, approximately 83.4% intron-containing genes were alternatively spliced. Two types, which referred first exon (AFE) last (ALE), more abundant than intron retention (IR); by contrast events detected under normal conditions, differentially expressed likely be translated. ABA extensively affects pattern, indicated increasing number non-conventional sites. This work also identified thousands peptides ATI based on mass spectrometry a virtual peptide library deduced both strands coding regions within Arabidopsis genome. The results enhance our understanding