Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L.
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 m...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-09-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.733505/full |
| _version_ | 1818662028851544064 |
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| author | Tingyu Ma Tingyu Ma Han Gao Han Gao Dong Zhang Dong Zhang 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 Li Xiang Shilin Chen |
| author_facet | Tingyu Ma Tingyu Ma Han Gao Han Gao Dong Zhang Dong Zhang 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 Li Xiang Shilin Chen |
| author_sort | Tingyu Ma |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T04:54:27Z |
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| id | doaj.art-c02f5ac3d82b43a8b8be75165e71e1b4 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-17T04:54:27Z |
| publishDate | 2021-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c02f5ac3d82b43a8b8be75165e71e1b42022-12-21T22:02:46ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-09-011210.3389/fpls.2021.733505733505Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L.Tingyu Ma0Tingyu Ma1Han Gao2Han Gao3Dong Zhang4Dong Zhang5Dong Zhang6Wei Sun7Qinggang Yin8Lan Wu9Tianyuan Zhang10Zhichao Xu11Jianhe Wei12Yanyan Su13Yuhua Shi14Dandan Ding15Ling Yuan16Gangqiang Dong17Liang Leng18Li Xiang19Li Xiang20Shilin Chen21Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaSchool of Life Sciences, Central China Normal University, Wuhan, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaHainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, ChinaAmway (China) Botanical R&D Center, Wuxi, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaDepartment of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United StatesAmway (China) Botanical R&D Center, Wuxi, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaDepartment of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United StatesKey Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaArtemisinin 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.https://www.frontiersin.org/articles/10.3389/fpls.2021.733505/fullArtemisia annuasingle molecule real-time (SMRT) sequencingalternative splicingintron retentionlight-regulatedartemisinin |
| spellingShingle | Tingyu Ma Tingyu Ma Han Gao Han Gao Dong Zhang Dong Zhang 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 Li Xiang Shilin Chen Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L. Frontiers in Plant Science Artemisia annua single molecule real-time (SMRT) sequencing alternative splicing intron retention light-regulated artemisinin |
| title | Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L. |
| title_full | Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L. |
| title_fullStr | Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L. |
| title_full_unstemmed | Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L. |
| title_short | Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L. |
| title_sort | genome wide analysis of light regulated alternative splicing in artemisia annua l |
| topic | Artemisia annua single molecule real-time (SMRT) sequencing alternative splicing intron retention light-regulated artemisinin |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.733505/full |
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