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Global Dissection of Alternative Splicing in Paleopolyploid Soybean
Yanting Shen,Zhengkui Zhou,Zheng Wang,Weiyu Li,Chao Fang,Mian Wu,Yanming Ma,Tengfei Liu,Ling-An Kong,De-Liang Peng and Zhixi Tian
The Plant Cell
Abstract
Alternative splicing ( AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean ( Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS.
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论文编号: |
DOI:10.1105/tpc.114.122739 |
论文题目: |
Global Dissection of Alternative Splicing in Paleopolyploid Soybean |
英文论文题目: |
Global Dissection of Alternative Splicing in Paleopolyploid Soybean |
第一作者: |
Yanting Shen,Zhengkui Zhou,Zheng Wang,Weiyu Li,Chao Fang,Mian Wu,Yanming Ma,Tengfei Liu,Ling-An Kong,De-Liang Peng and Zhixi Tian |
英文第一作者: |
Yanting Shen,Zhengkui Zhou,Zheng Wang,Weiyu Li,Chao Fang,Mian Wu,Yanming Ma,Tengfei Liu,Ling-An Kong,De-Liang Peng and Zhixi Tian |
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2014-03-31 |
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摘要: |
Alternative splicing ( AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean ( Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS. |
英文摘要: |
Alternative splicing ( AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean ( Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS. |
刊物名称: |
The Plant Cell |
英文刊物名称: |
The Plant Cell |
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其它备注: |
Yanting Shen,Zhengkui Zhou,Zheng Wang,Weiyu Li,Chao Fang,Mian Wu,Yanming Ma,Tengfei Liu,Ling-An Kong,De-Liang Peng and Zhixi Tian. Global Dissection of Alternative Splicing in Paleopolyploid Soybean. The Plant Cell. DOI:10.1105/tpc.114.122739 |
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