Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis)
Abstract Background Alternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms. However, little is known about the AS and its roles in tea plant (Camellia sinensis), widely cultivated for making a popular beverage tea. Results In our study, the AS...
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-018-1497-9 |
| _version_ | 1818027741351510016 |
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| author | Junyan Zhu Xuewen Wang Qingshan Xu Shiqi Zhao Yuling Tai Chaoling Wei |
| author_facet | Junyan Zhu Xuewen Wang Qingshan Xu Shiqi Zhao Yuling Tai Chaoling Wei |
| author_sort | Junyan Zhu |
| collection | DOAJ |
| description | Abstract Background Alternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms. However, little is known about the AS and its roles in tea plant (Camellia sinensis), widely cultivated for making a popular beverage tea. Results In our study, the AS landscape and dynamics were characterized in eight tissues (bud, young leaf, summer mature leaf, winter old leaf, stem, root, flower, fruit) of tea plant by Illumina RNA-Seq and confirmed by Iso-Seq. The most abundant AS (~ 20%) was intron retention and involved in RNA processes. The some alternative splicings were found to be tissue specific in stem and root etc. Thirteen co-expressed modules of AS transcripts were identified, which revealed a similar pattern between the bud and young leaves as well as a distinct pattern between seasons. AS events of structural genes including anthocyanidin reductase and MYB transcription factors were involved in biosynthesis of flavonoid, especially in vegetative tissues. The AS isoforms rather than the full-length ones were the major transcripts involved in flavonoid synthesis pathway, and is positively correlated with the catechins content conferring the tea taste. We propose that the AS is an important functional mechanism in regulating flavonoid metabolites. Conclusion Our study provides the insight into the AS events underlying tea plant’s uniquely different developmental process and highlights the important contribution and efficacy of alternative splicing regulatory function to biosynthesis of flavonoids. |
| first_indexed | 2024-12-10T04:52:43Z |
| format | Article |
| id | doaj.art-c7e74b4f4bb944c69369fd18557006de |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-10T04:52:43Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj.art-c7e74b4f4bb944c69369fd18557006de2022-12-22T02:01:35ZengBMCBMC Plant Biology1471-22292018-11-0118111210.1186/s12870-018-1497-9Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis)Junyan Zhu0Xuewen Wang1Qingshan Xu2Shiqi Zhao3Yuling Tai4Chaoling Wei5State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural UniversityState Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural UniversityState Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural UniversityState Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural UniversityState Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural UniversityState Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural UniversityAbstract Background Alternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms. However, little is known about the AS and its roles in tea plant (Camellia sinensis), widely cultivated for making a popular beverage tea. Results In our study, the AS landscape and dynamics were characterized in eight tissues (bud, young leaf, summer mature leaf, winter old leaf, stem, root, flower, fruit) of tea plant by Illumina RNA-Seq and confirmed by Iso-Seq. The most abundant AS (~ 20%) was intron retention and involved in RNA processes. The some alternative splicings were found to be tissue specific in stem and root etc. Thirteen co-expressed modules of AS transcripts were identified, which revealed a similar pattern between the bud and young leaves as well as a distinct pattern between seasons. AS events of structural genes including anthocyanidin reductase and MYB transcription factors were involved in biosynthesis of flavonoid, especially in vegetative tissues. The AS isoforms rather than the full-length ones were the major transcripts involved in flavonoid synthesis pathway, and is positively correlated with the catechins content conferring the tea taste. We propose that the AS is an important functional mechanism in regulating flavonoid metabolites. Conclusion Our study provides the insight into the AS events underlying tea plant’s uniquely different developmental process and highlights the important contribution and efficacy of alternative splicing regulatory function to biosynthesis of flavonoids.http://link.springer.com/article/10.1186/s12870-018-1497-9Alternative splicingCamellia sinensisTissue-specificityFlavonoid |
| spellingShingle | Junyan Zhu Xuewen Wang Qingshan Xu Shiqi Zhao Yuling Tai Chaoling Wei Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis) BMC Plant Biology Alternative splicing Camellia sinensis Tissue-specificity Flavonoid |
| title | Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis) |
| title_full | Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis) |
| title_fullStr | Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis) |
| title_full_unstemmed | Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis) |
| title_short | Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis) |
| title_sort | global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant camellia sinensis |
| topic | Alternative splicing Camellia sinensis Tissue-specificity Flavonoid |
| url | http://link.springer.com/article/10.1186/s12870-018-1497-9 |
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