Data_Sheet_2_Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L..PDF

Artemisinin is currently the most effective ingredient in the treatment of malaria, which is thus of great significance to study the genetic regulation of Artemisia annua. Alternative splicing (AS) is a regulatory process that increases the complexity of transcriptome and proteome. The most common mechanism of alternative splicing (AS) in plant is intron retention (IR). However, little is known about whether the IR isoforms produced by light play roles in regulating biosynthetic pathways. In this work we would explore how the level of AS in A. annua responds to light regulation. We obtained a new dataset of AS by analyzing full-length transcripts using both Illumina- and single molecule real-time (SMRT)-based RNA-seq as well as analyzing AS on various tissues. A total of 5,854 IR isoforms were identified, with IR accounting for the highest proportion (48.48%), affirming that IR is the most common mechanism of AS. We found that the number of up-regulated IR isoforms (1534/1378, blue and red light, respectively) was more than twice that of down-regulated (636/682) after treatment of blue or red light. In the artemisinin biosynthetic pathway, 10 genes produced 16 differentially expressed IR isoforms. This work demonstrated that the differential expression of IR isoforms induced by light has the potential to regulate sesquiterpenoid biosynthesis. This study also provides high accuracy full-length transcripts, which can be a valuable genetic resource for further research of A. annua, including areas of development, breeding, and biosynthesis of active compounds.

青蒿素（Artemisinin）是当前治疗疟疾的最优成分，因此对黄花蒿（Artemisia annua）的基因调控机制开展研究具有重要价值。可变剪接（Alternative splicing, AS）是一类提升转录组与蛋白质组复杂度的调控过程。植物中最为常见的可变剪接机制为内含子保留（Intron retention, IR）。但目前对于光照诱导产生的内含子保留转录本是否参与调控生物合成通路仍知之甚少。本研究旨在探究黄花蒿体内的可变剪接水平如何响应光照调控。我们通过结合基于Illumina平台与单分子实时（single molecule real-time, SMRT）测序的RNA测序（RNA-seq）技术分析全长转录本，并对不同组织的可变剪接情况进行分析，获得了一套全新的可变剪接数据集。本研究共鉴定得到5854个内含子保留转录本，内含子保留占比达48.48%，证实内含子保留是植物中最常见的可变剪接机制。我们发现，经蓝光或红光处理后，上调表达的内含子保留转录本数量（蓝光、红光处理组分别为1534、1378）是下调表达组（636、682）的两倍以上。在青蒿素生物合成通路中，10个基因共产生16个差异表达的内含子保留转录本。本研究证实，光照诱导的内含子保留转录本差异表达具备调控倍半萜类（sesquiterpenoid）生物合成的潜力。本研究还提供了高精度的全长转录本数据，可为黄花蒿后续的发育研究、育种工作以及活性成分生物合成等领域提供宝贵的遗传资源。