Genome-wide Transcriptome and Proteome Profiling Indicate an Active Role of Alternative Splicing During De-etiolation of Maize Seedlings

To decipher the effects of various wavelengths of light on de-etiolation, we illuminated etiolated maize seedlings with blue, red, blue-red mixed and white light. We found that blue light alone has the strongest effect on photomorphogenic development based on several physiological indices and it can be attributed to the higher number and expression levels of photosynthesis and chlorosynthesis proteins. Deep sequencing-based transcriptome analysis revealed gene expression changes under different light treatments and a genome-wide alteration in alternative splicing (AS) profiles. We discovered 41,188 novel transcript isoforms for annotated genes, which increases the percentage of multi-exon genes with AS to 63% in maize.