Accession PRJCA001736
Title Genome-wide Transcriptome and Proteome Profiling Indicate an Active Role of Alternative Splicing During De-etiolation of Maize Seedlings
Relevance Agricultural
Data types Transcriptome or Gene expression
Organisms Zea mays
Description 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. We discovered 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.
Sample scope Multiisolate
Release date 2020-06-30
Grants
Agency program Grant ID Grant title
Ministry of Science and Technology of the People's Republic of China (MOST) 2016YFD0101003
National Natural Science Foundation of China (NSFC) 31030017
Chinese Academy of Sciences (CAS) XDA08010206.5
Submitter Zhen    Yan  (yanzhensky@ibcas.ac.cn)
Organization Institute of Botany, Chinese Academy of Sciences
Submission date 2019-09-10

Project Data

Resource name Description
BioSample (26)  show -
GSA (1) -
CRA001961 Genome-wide Transcriptome and Proteome Profiling Indicate an Active Role of Alternative Splicing During De-etiolation of Maize Seedlings