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

Tingyu Ma,Shilin Chen,Dandan Ding,Jianhe Wei,Yuhua Shi,Li Xiang,Gangqiang Dong,Dong Zhang,Qinggang Yin,Zhichao Xu,Lan Wu,Liang Leng,Wei Sun,Ling Yuan,Yanyan Su,Han Gao,Tianyuan Zhang

doi:10.3389/fpls.2021.733505

Abstract

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.

Highlights

The main natural source of Artemisinin, a sesquiterpene lactone with peroxide bridge, is the medicinal herb Artemisia annua (Miller and Su, 2011; Tu, 2011)
We compared the AS genes we identified with genes predicted to be involved in the biosynthesis pathway for the general sesquiterpenes precursor FPP and artemisinin synthesis
The accumulation of artemisinin is unique in A. annua, and the yield of artemisinin largely determines the medicinal value of A. annua (Graham et al, 2010; Czechowski et al, 2016, 2018)

Summary

Introduction

The main natural source of Artemisinin, a sesquiterpene lactone with peroxide bridge, is the medicinal herb Artemisia annua (Miller and Su, 2011; Tu, 2011). Artemisinin is famous for its role in artemisinin combination therapies (ACT), the most effective malaria treatment currently available (Czechowski et al, 2016). Development of new uses of artemisinin and its derivatives, e.g., dihydroartemisinin in the treatment of systemic lupus erythematosus, is still ongoing. These efforts show some potential in anti-tumor, anti-parasitic, anti-fibrosis, and antiarrhythmic effects (Bin and Hong, 2010). Biosynthesis and chemical synthesis of Artemisinin have seen significant progress in recent years, the final steps in the conversion of dihydroartemisinic acid (DHAA) to artemisinin are still non-enzymatic and require extracellular treatments (Graham et al, 2010; Czechowski et al, 2016). In molecular analysis, are needed to understand the biology of A. annua in order to improve artemisinin content of the plant and to reduce production cost

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