PXD014602

PXD014602 is an original dataset announced via ProteomeXchange.

Title	Genome-wide Transcriptome and Proteome Profiling Indicate an Active Role of Alternative Splicing During De-etiolation of Maize Seedlings
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. 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.
HostingRepository	iProX
AnnounceDate	2019-07-14
AnnouncementXML	Submission_2023-08-27_21:07:28.973.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tiancong Lu
SpeciesList	scientific name: Zea mays; NCBI TaxID: 4577;
ModificationList	iTRAQ4plex reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-14 19:50:17	ID requested
1	2019-07-14 19:53:32	announced
2	2019-07-16 02:28:37	announced	Update information.
⏵ 3	2023-08-27 21:07:29	announced	2019-07-16: Update information. 2023-08-28: Update publication information.

Yan Z, Shen Z, Li Z, Chao Q, Kong L, Gao ZF, Li QW, Zheng HY, Zhao CF, Lu CM, Wang YW, Wang BC, Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings. Planta, 252(4):60(2020) [pubmed]

submitter keyword: Transcriptome, Alternative splicing

Proteome, De-etiolation, Maize seedlings

Baichen Wang
contact affiliation	Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
contact email	wangbc@ibcas.ac.cn
lab head
Tiancong Lu
contact affiliation	Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
contact email	proteomelandscape@163.com
dataset submitter

iProX dataset URI