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

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

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

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.

Original languageEnglish
Article number733505
JournalFrontiers in Plant Science
Volume12
DOIs
StatePublished - Sep 29 2021

Bibliographical note

Funding Information:
We would like to thank Yujun Zhang from Institute of the China Academy of Chinese Medical Sciences for the helpful discussion.

Funding Information:
This work was supported by the National Natural Science Foundation of China and Karst Science Research Center of Guizhou Province (U1812403-1), the China Postdoctoral Science Foundation (2021M690464), the National Natural Science Foundation of China (81903758, 31900258, and 81641002), the National Major Science and Technology Projects (2017ZX09101002-003-001, 2019ZX09201005-006-001, and 2019ZX09731-002), and the CACMS Innovation Fund (CI2021A05103).

Publisher Copyright:
© Copyright © 2021 Ma, Gao, Zhang, Sun, Yin, Wu, Zhang, Xu, Wei, Su, Shi, Ding, Yuan, Dong, Leng, Xiang and Chen.

Keywords

  • Artemisia annua
  • alternative splicing
  • artemisinin
  • intron retention
  • light-regulated
  • single molecule real-time (SMRT) sequencing

ASJC Scopus subject areas

  • Plant Science

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