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. 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.

中文翻译：

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全基因组转录组和蛋白质组谱表明选择性剪接在玉米幼苗去黄化过程中的积极作用

主要结论 AS事件影响编码蛋白质结构域组成的基因，使单个基因产生更多具有一定数量基因的蛋白质，以满足去黄化过程中光合作用的建立。从 skotomorphogenic 到 photomorphogenic 发育的剧烈转变是阐明植物对环境刺激的快速发育反应的极好系统。为了破译不同光波长对去黄化的影响，我们分别用蓝光、红光、蓝红混合光和白光照射黄化玉米幼苗。我们发现单独的蓝光对光形态发生的影响最强，这种影响可归因于光合作用和氯合作用蛋白的数量和表达水平较高。基于深度测序的转录组分析揭示了不同光照处理下的基因表达变化以及选择性剪接 (AS) 谱的全基因组变化。我们发现了 41,188 个新的注释基因转录亚型，这将玉米中具有 AS 的多外显子基因的百分比增加到 63%。我们为所有定义类型的 AS 提供肽支持，尤其是保留的内含子。进一步的计算机预测显示，与其最相似的注释蛋白质异构体相比，58.2% 的保留内含子在结构域中发生了变化。这表明 AS 充当蛋白质功能开关，通过添加或去除功能域允许快速光响应。