Alternative splicing and translation play important roles in parallel with transcriptional regulation during rice hypoxic germination

Abstract

9Post-transcriptional mechanisms, including alternative splicing (AS) and alternative 4 0 translation initiation (ATI), have been used to explain the protein diversity involved in 4 1 plant developmental processes and stress responses. Rice germination under hypoxia 4 2conditions is a classical model system for the study of low oxygen stress. It is known 4 3 that there is transcriptional regulation during rice hypoxic germination, but the 4 4 potential roles of AS and ATI in this process are not well understood. In this study, a 4 5proteogenomic approach was used to integrate the data from RNA sequencing, 4 6qualitative and quantitative proteomics to discover new players or pathways in the 4 7response to hypoxia stress. The improved analytical pipeline of proteogenomics led to 4 8the identification of 10,253 intron-containing genes, 1,729 of which were not present 4 9