Alternative Splicing under Cold Stress in Paper Mulberry
The paper mulberry is a commonly found tree species with a long history of cultivation. It also serves as a crucial case study for understanding how woody plants adapt to low temperatures. Under cold treatment, we observed a substantial number of alternative splicing (AS) genes, showcasing the intri...
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MDPI AG
2023-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/23/3950 |
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| author | Zhipeng Yu Xia Huang Shuhan Wen Haijuan Cao Nan Wang Shihua Shen Mingquan Ding |
| author_facet | Zhipeng Yu Xia Huang Shuhan Wen Haijuan Cao Nan Wang Shihua Shen Mingquan Ding |
| author_sort | Zhipeng Yu |
| collection | DOAJ |
| description | The paper mulberry is a commonly found tree species with a long history of cultivation. It also serves as a crucial case study for understanding how woody plants adapt to low temperatures. Under cold treatment, we observed a substantial number of alternative splicing (AS) genes, showcasing the intricate landscape of AS events. We have detected all seven types of AS events, with the alternative 3′ splice site (A3) having the most. We observed that many genes that underwent differential AS were significantly enriched in starch and sucrose metabolism and circadian rhythm pathways. Moreover, a considerable proportion of differentially spliced genes (DSGs) also showed differential expression, with 20.38% and 25.65% under 12 h and 24 h cold treatments, respectively. This suggests a coordinated regulation between gene AS and expression, playing a pivotal role in the paper mulberry’s adaptation to cold stress. We further investigated the regulatory mechanisms of AS, identifying 41 serine/arginine-rich (SR) splicing factors, among which 11 showed differential expression under cold treatment, while 29 underwent alternative splicing. Additionally, genes undergoing AS displayed significantly higher DNA methylation levels under cold stress, while normal splicing (non-AS) genes exhibited relatively lower methylation levels. These findings suggest that methylation may play an important role in governing gene AS. Finally, our research will provide useful information on the role of AS in the cold acclimation tolerance of the paper mulberry. |
| first_indexed | 2024-03-09T01:45:01Z |
| format | Article |
| id | doaj.art-73387c7c3ff5407389caefbde46257fb |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T01:45:01Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-73387c7c3ff5407389caefbde46257fb2023-12-08T15:23:44ZengMDPI AGPlants2223-77472023-11-011223395010.3390/plants12233950Alternative Splicing under Cold Stress in Paper MulberryZhipeng Yu0Xia Huang1Shuhan Wen2Haijuan Cao3Nan Wang4Shihua Shen5Mingquan Ding6The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaState Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe paper mulberry is a commonly found tree species with a long history of cultivation. It also serves as a crucial case study for understanding how woody plants adapt to low temperatures. Under cold treatment, we observed a substantial number of alternative splicing (AS) genes, showcasing the intricate landscape of AS events. We have detected all seven types of AS events, with the alternative 3′ splice site (A3) having the most. We observed that many genes that underwent differential AS were significantly enriched in starch and sucrose metabolism and circadian rhythm pathways. Moreover, a considerable proportion of differentially spliced genes (DSGs) also showed differential expression, with 20.38% and 25.65% under 12 h and 24 h cold treatments, respectively. This suggests a coordinated regulation between gene AS and expression, playing a pivotal role in the paper mulberry’s adaptation to cold stress. We further investigated the regulatory mechanisms of AS, identifying 41 serine/arginine-rich (SR) splicing factors, among which 11 showed differential expression under cold treatment, while 29 underwent alternative splicing. Additionally, genes undergoing AS displayed significantly higher DNA methylation levels under cold stress, while normal splicing (non-AS) genes exhibited relatively lower methylation levels. These findings suggest that methylation may play an important role in governing gene AS. Finally, our research will provide useful information on the role of AS in the cold acclimation tolerance of the paper mulberry.https://www.mdpi.com/2223-7747/12/23/3950paper mulberryalternative splicingdifferentially spliced genescold stressDNA methylation |
| spellingShingle | Zhipeng Yu Xia Huang Shuhan Wen Haijuan Cao Nan Wang Shihua Shen Mingquan Ding Alternative Splicing under Cold Stress in Paper Mulberry Plants paper mulberry alternative splicing differentially spliced genes cold stress DNA methylation |
| title | Alternative Splicing under Cold Stress in Paper Mulberry |
| title_full | Alternative Splicing under Cold Stress in Paper Mulberry |
| title_fullStr | Alternative Splicing under Cold Stress in Paper Mulberry |
| title_full_unstemmed | Alternative Splicing under Cold Stress in Paper Mulberry |
| title_short | Alternative Splicing under Cold Stress in Paper Mulberry |
| title_sort | alternative splicing under cold stress in paper mulberry |
| topic | paper mulberry alternative splicing differentially spliced genes cold stress DNA methylation |
| url | https://www.mdpi.com/2223-7747/12/23/3950 |
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