Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis
In eukaryotes, alternative splicing (AS) is one of the posttranscriptional regulatory mechanisms that play important roles by generating transcriptome diversity. To obtain a global view of AS and its dynamics during tomato fruit development, we analyzed the AS events using a large amount of transcri...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2016-11-01
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| Series: | Horticultural Plant Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468014117300080 |
| _version_ | 1827280448527532032 |
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| author | Ketao Wang Zhicheng Jiao Meng Xu Yongsheng Wang Ren Li Xia Cui Lianfeng Gu Shuaibin Zhang |
| author_facet | Ketao Wang Zhicheng Jiao Meng Xu Yongsheng Wang Ren Li Xia Cui Lianfeng Gu Shuaibin Zhang |
| author_sort | Ketao Wang |
| collection | DOAJ |
| description | In eukaryotes, alternative splicing (AS) is one of the posttranscriptional regulatory mechanisms that play important roles by generating transcriptome diversity. To obtain a global view of AS and its dynamics during tomato fruit development, we analyzed the AS events using a large amount of transcriptome datasets. Same with other plant species, about half of the expressed multiexonic genes were alternatively spliced in tomato. Besides that, our further analyzation of RNA-seq datasets of ovule and pericarp at early fruit developmental stages reveals that the dynamic alteration of AS events occurred in specific tissues and AS was regulated spatially and temporally during early fruit development in tomato. By investigating the sequence variations at splice sites causing differential AS events between tomato cultivar ‘Moneymaker’ and wild species Solanum pimpinellifolium PI365967, we uncover that AS may play the regulatory roles during domestication of tomato. Taken together, our results provided the global AS pattern in tomato and highlighted the importance of AS during tomato fruit development and domestication. |
| first_indexed | 2024-04-24T08:41:24Z |
| format | Article |
| id | doaj.art-b0bceaf607bf46aab32ade613d5e30bf |
| institution | Directory Open Access Journal |
| issn | 2468-0141 |
| language | English |
| last_indexed | 2024-04-24T08:41:24Z |
| publishDate | 2016-11-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Horticultural Plant Journal |
| spelling | doaj.art-b0bceaf607bf46aab32ade613d5e30bf2024-04-16T16:12:10ZengKeAi Communications Co., Ltd.Horticultural Plant Journal2468-01412016-11-012633835010.1016/j.hpj.2017.01.007Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide AnalysisKetao Wang0Zhicheng Jiao1Meng Xu2Yongsheng Wang3Ren Li4Xia Cui5Lianfeng Gu6Shuaibin Zhang7Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaHaixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaHaixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaIn eukaryotes, alternative splicing (AS) is one of the posttranscriptional regulatory mechanisms that play important roles by generating transcriptome diversity. To obtain a global view of AS and its dynamics during tomato fruit development, we analyzed the AS events using a large amount of transcriptome datasets. Same with other plant species, about half of the expressed multiexonic genes were alternatively spliced in tomato. Besides that, our further analyzation of RNA-seq datasets of ovule and pericarp at early fruit developmental stages reveals that the dynamic alteration of AS events occurred in specific tissues and AS was regulated spatially and temporally during early fruit development in tomato. By investigating the sequence variations at splice sites causing differential AS events between tomato cultivar ‘Moneymaker’ and wild species Solanum pimpinellifolium PI365967, we uncover that AS may play the regulatory roles during domestication of tomato. Taken together, our results provided the global AS pattern in tomato and highlighted the importance of AS during tomato fruit development and domestication.http://www.sciencedirect.com/science/article/pii/S2468014117300080tomatoalternative splicing (AS)fruit developmentdomestication |
| spellingShingle | Ketao Wang Zhicheng Jiao Meng Xu Yongsheng Wang Ren Li Xia Cui Lianfeng Gu Shuaibin Zhang Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis Horticultural Plant Journal tomato alternative splicing (AS) fruit development domestication |
| title | Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis |
| title_full | Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis |
| title_fullStr | Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis |
| title_full_unstemmed | Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis |
| title_short | Landscape and Fruit Developmental Regulation of Alternative Splicing in Tomato by Genome-Wide Analysis |
| title_sort | landscape and fruit developmental regulation of alternative splicing in tomato by genome wide analysis |
| topic | tomato alternative splicing (AS) fruit development domestication |
| url | http://www.sciencedirect.com/science/article/pii/S2468014117300080 |
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