Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of
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ORIGINAL ARTICLE
Genome‑wide transcriptome and proteome profiles indicate an active role of alternative splicing during de‑etiolation of maize seedlings Zhen Yan1,2 · Zhuo Shen3 · Zhe Li4 · Qing Chao1,2,9 · Lei Kong5 · Zhi‑Fang Gao1 · Qing‑Wei Li6 · Hai‑Yan Zheng7 · Cai‑Feng Zhao7 · Cong‑Ming Lu8 · Ying‑Wei Wang6 · Bai‑Chen Wang1,2,9 Received: 22 May 2020 / Accepted: 12 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Main 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. Abstract 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. Keywords Alternative splicing · De-etiolation · Maize seedlings · Proteome · Transcriptome Abbreviations AS Alternative splicing BP Biological process CC Cellular component DEG Differentially expressed protein DEU Differential exon usage Communicated by Dorothea Bartels. Zhen Yan, Zhuo Shen and Zhe Li contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00425-020-03464-5) contains supplementary material, which is available to authorized users. * Ying‑Wei Wang [email protected] * Bai‑Chen Wang [email protected] Extended author information available on the last page of the article
GO Gene ontology MF Molecular function NTR Novel transcript region PTC Premature termination codon
Introduction Light perception and signalling have a great impact on plant growth (Jiao et al. 2007). The switch from skotomorphogenesis (dark-adapted development) to photomorp
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