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

ABSTRACT: The dramatic switch from skotomorphogenic to photomorphogenic development is an excellent system to elucidate both light signal transduction pathways and rapid developmental response to environmental stimuli in plants. 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. Wed is covered 41,188 novel transcript isoforms for annotated genes, which increases the percentage of multi-exon genes with AS to 63% in maize. We provide peptide support for all defined types of AS, especially retained introns. And further in silico prediction reveals that 58.2% of retained introns have changes in domains compared to their most similar annotated protein isoform. This suggests that AS is an important mechanism for increasing protein diversity and acts as a protein function switch allowing rapid light response through the addition or removal of functional domains. The richness of novel transcripts and protein isoforms also demonstrates the potential and importance of integrating proteomics into genome annotation in maize.

ORGANISM(S): Zea Mays

SUBMITTER: Baichen Wang  

PROVIDER: PXD014602 | iProX | Sun Jul 14 00:00:00 BST 2019

REPOSITORIES: iProX