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Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings
Yan, Zhen; Shen, Zhuo2; Li, Zhe3; Chao, Qing; Kong, Lei4; Gao, Zhi-Fang; Li, Qing-Wei; Zheng, Hai-Yan; Zhao, Cai-Feng; Lu, Cong-Ming; Wang, Ying-Wei; Wang, Bai-Chen
Source PublicationPLANTA
AbstractMain conclusion AS events affect genes encoding protein domain composition and make the single gene produce more proteins with a certain number of genes to satisfy the establishment of photosynthesis during de-etiolation. The drastic switch from skotomorphogenic to photomorphogenic development is an excellent system to elucidate rapid developmental responses to environmental stimuli in plants. To decipher the effects of different light wavelengths on de-etiolation, we illuminated etiolated maize seedlings with blue, red, blue-red mixed and white light, respectively. We found that blue light alone has the strongest effect on photomorphogenesis and that this effect 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. Further in silico prediction revealed that 58.2% of retained introns have changes in domains compared with their most similar annotated protein isoform. This suggests that AS 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.
KeywordAlternative splicing De-etiolation Maize seedlings Proteome Transcriptome
Subject AreaPlant Sciences
Indexed BySCI
WOS Research AreaPlant Sciences
WOS IDWOS:000574591400002
Publication PlaceNEW YORK
Funding OrganizationStrategic Priority Research Program of the Chinese Academy of SciencesChinese Academy of Sciences [XDA24010203] ; National Key Research and Development Program of China [2016YFD0101003]
Corresponding Author Emailywwang@ibcas.ac.cn ; wangbc@ibcas.ac.cn
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Document Type期刊论文
Affiliation1.Chinese Acad Sci, Photosynth Res Ctr, Inst Bot, Key Lab Photobiol, 20 Nanxincun, Beijing 100093, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Guangdong Acad Agr Sci, Vegetable Res Inst, Guangdong Key Lab New Technol Res Vegetables, Guangzhou 510640, Peoples R China
4.Precis Sci Beijing Co Ltd, Beijing 100085, Peoples R China
5.Peking Univ, Coll Life Sci, Ctr Bioinformat, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China
6.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing 100093, Peoples R China
7.Rutgers State Univ, Ctr Adv Biotechnol & Med, Biol Mass Spectrometry Facil, Piscataway, NJ 08855 USA
8.Shandong Agr Univ, Coll Life Sci, State Key Lab Crop Biol, Tai An 271018, Shandong, Peoples R China
9.Chinese Acad Sci, Innovat Acad Seed Design, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Yan, Zhen,Shen, Zhuo,Li, Zhe,et al. Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings[J]. PLANTA,2020,252(4).
APA Yan, Zhen.,Shen, Zhuo.,Li, Zhe.,Chao, Qing.,Kong, Lei.,...&Wang, Bai-Chen.(2020).Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings.PLANTA,252(4).
MLA Yan, Zhen,et al."Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings".PLANTA 252.4(2020).
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