The comparison of alternative splicing among the multiple tissues in cucumber

文献类型： 外文期刊

第一作者： Sun, Ying

作者： Sun, Ying;Song, Hongtao;Lin, Kui;Pang, Erli;Sun, Ying;Song, Hongtao;Lin, Kui;Pang, Erli;Hou, Han;Zhang, Zhonghua;Hou, Han;Hu, Jinglu

作者机构：

关键词： Alternative splicing;Tissues;Tissue-specific;Cucumber

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2018 年 18 卷

页码：

收录情况： SCI

摘要： Background: Alternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tissues are poorly explored. Results: To analyse global changes in AS in multiple tissues, we identified the AS events and constructed a comprehensive catalogue of AS events within each tissue based on the genome-wide RNA-seq reads from ten tissues in cucumber. First, we found that 58% of the multi-exon genes underwent AS. We further obtained 565 genes with significantly more AS events compared with random genes. These genes were found significant enrichment in biological processes related to the regulation of actin filament length. Second, significantly different AS event profiles among ten tissues were found. The tissues with the same origin of development are more likely to have a relatively similar AS profile. Moreover, 7370 genes showed tissue-specific AS events and were highly enriched in biological processes related to the positive regulation of cellular component organization. Root-specificity AS genes were related to the cellular response to DNA damage stimulus. Third, the genes with different intron retention (IR) patterns among the ten tissues showed significant difference in GC percentages of the retained intron, and the number of exons and FPKM of the major transcripts. Conclusions: Our study provided a comprehensive view of AS in multiple tissues. We revealed novel insights into the patterns of AS in multiple tissues and the tissue-specific AS in cucumber.

分类号：

  • 相关文献

[1]Cloning and Characterization of New Splice Variants of Insulin-Like Growth Factor-1 Gene in Songliao Black Pig. Liu, Chang,Zhaoa, Zhihui,Bai, Wenlin,Sun, Boxing,Zhang, Yonghong,Yang, Runjun,Liu, Chang,Bai, Wenlin. 2012

[2]Large-scale tissue-specific and temporal gene expression profiles in Pengze crucian carp. Zheng, Y.,Chen, J. Z.,Bing, X. W.,Zheng, Y.,Chen, J. Z.,Bing, X. W.,Zheng, Y.,Wang, H. P.,Li, M.,Wang, Z. Z.,Liang, H. W.. 2016

[3]Different Virus-Derived siRNAs Profiles between Leaves and Fruits in Cucumber Green Mottle MosaicVirus-In fected Lagenaria siceraria Plants. Li, Junmin,Zheng, Hongying,Zhang, Chenhua,Han, Kelei,Wang, Shu,Peng, Jiejun,Lu, Yuwen,Zhao, Jinping,Xu, Pei,Wu, Xiaohua,Li, Guojing,Chen, Jianping,Yan, Fei,Li, Junmin,Zheng, Hongying,Han, Kelei,Peng, Jiejun,Lu, Yuwen,Zhao, Jinping,Chen, Jianping,Yan, Fei,Zhang, Chenhua,Chen, Jianping,Xu, Pei,Wu, Xiaohua,Li, Guojing. 2016

[4]Isolation of a maize ZmCI-1B promoter and characterization of its activity in transgenic maize and tobacco. Li, Ye,Liu, Xiaoqing,Zhou, Xiaojin,Yang, Wenzhu,Chen, Rumei,Li, Jie,Li, Suzhen,Chen, Guanyu.

[5]Chicken RNA-binding protein T-cell internal antigen-1 contributes to stress granule formation in chicken cells and tissues. Sun, Yingjie,Tan, Lei,Song, Cuiping,Qiu, Xusheng,Liao, Ying,Meng, Chunchun,Yu, Shengqing,Ding, Chan,Zhang, Pin,Zheng, Hang,Dong, Luna,Ding, Chan. 2018

[6]Simultaneous qualitative assessment and quantitative analysis of flavonoids in various tissues of lotus (Nelumbo nucifera) using high performance liquid chromatography coupled with triple quad mass spectrometry. Chen, Sha,Xi, Huifen,Guan, Le,Wu, Benhong,Chen, Sha,Xi, Huifen,Guan, Le,Wu, Benhong,Chen, Sha,Fang, Linchuan,Liu, Yanling,Li, Shaohua,Chen, Sha,Fang, Jinbao.

[7]Simultaneous determination of residues of dipyrone metabolites in goat tissues by hydrophilic interaction liquid chromatography tandem mass spectrometry. Zhang, Chong,Zhang, Lifang,Jiang, Zhaoling,Zhang, Xiaoxiao,Xue, Feiqun,Zhang, Chong,Cao, Suqing,Wu, Hao,Yan, Ming,Jiang, Shanxiang.

[8]Regulation of Anthocyanin Biosynthesis in Tissues of a Teinturier Grape Cultivar under Sunlight Exclusion. Guan, Le,Li, Ji-Hu,Fan, Pei-Ge,Wang, Li-Jun,Wu, Ben-Hong,Guan, Le,Li, Ji-Hu,Fan, Pei-Ge,Wang, Li-Jun,Wu, Ben-Hong,Li, Shao-Hua,Fang, Jin-Bao,Dai, Zhan-Wu,Delrot, Serge.

[9]Subcellular distribution of trace elements in kidney of a mother-fetus pair of Dall's porpoises (Phocoenoides dalli). Yang, Jian,Yang, Jian,Miyazaki, Nobuyuki,Kunito, Takashi,Anan, Yasumi,Tanabe, Shinsuke.

[10]Zinc and copper bioaccumulation in fish from Laizhou Bay, the Bohai Sea. Liu Jinhu,Cao Liang,Dou Shuozeng,Liu Jinhu,Huang Wei,Zhang Chuantao. 2014

[11]A novel splice variant of the bovine GALNTL5 gene identified in Chinese Holstein bull testis tissue and its mRNA expression. Li, H.,Jiang, Q.,Ju, Z. H.,Huang, J. M.,Wang, X. G.,Yang, C. H.,Sun, Y.,Zhong, J. F.,Wang, C. F.,Li, H.,Yang, G. W.. 2016

[12]A SNP in intron 8 of CD46 causes a novel transcript associated with mastitis in Holsteins. Wang, Xiuge,Zhong, Jifeng,Gao, Yundong,Ju, Zhihua,Huang, Jinming,Huang, Jinming. 2014

[13]Increased expression of a novel splice variant of the complement component 4 (C4A) gene in mastitis-infected dairy cattle. Yang, Y.,Huang, J. M.,Ju, Z. H.,Li, Q. L.,Zhou, L.,Li, R. L.,Li, J. B.,Zhong, J. F.,Wang, C. F.,Yang, Y.,Shi, F. X.,Yang, Y.. 2012

[14]Two splice variants of the bovine lactoferrin gene identified in Staphylococcus aureus isolated from mastitis in dairy cattle. Huang, J. M.,Wang, Z. Y.,Ju, Z. H.,Wang, C. F.,Li, Q. L.,Sun, T.,Hou, Q. L.,Hang, S. Q.,Hou, M. H.,Zhong, J. F.. 2011

[15]Novel splice variants of the bovine PCK1 gene. Zhang, Z. B.,Zhao, Z. S.,Huang, J. M.,Zhang, Z. B.,Zhang, W.,Li, R. L.,Li, J. B.,Zhong, J. F.. 2013

[16]Alternative splicing and mRNA expression analysis of bovine SLAMF7 gene in healthy and mastitis mammary tissues. Ju, Zhihua,Wang, Changfa,Li, Qiuling,Hou, Minghai,Gao, Shuai,Hou, Qinlei,Li, Jianbin,Huang, Jinming,Zhong, Jifeng.

[17]Functional defect at the rice choline monooxygenase locus from an unusual post-transcriptional processing is associated with the sequence elements of short-direct repeats. Niu, Xiangli,Wang, Yuguo,Zheng, Wenjing,Chang, Lijuan,Wang, Qilin,Wei, Xin,Yu, Guirong,Lu, Bao-Rong,Liu, Yongsheng. 2007

[18]Apple NPR1 homologs and their alternative splicing forms may contribute to SA and disease responses. Zhang, Junke,Wei, Qinping,Zhang, Junke,Wei, Qinping,Jiao, Peng,Zhang, Chong,Tong, Xiaolei,Xu, Lingfei. 2016

[19]Transcriptional and post-transcriptional regulation of the jasmonate signalling pathway in response to abiotic and harvesting stress in Hevea brasiliensis. Pirrello, Julien,Leclercq, Julie,Dessailly, Florence,Rio, Maryannick,Piyatrakul, Piyanuch,Montoro, Pascal,Piyatrakul, Piyanuch,Kuswanhadi, Kuswanhadi,Tang, Chaorong. 2014

[20]Identification of novel transcripts from the porcine MYL1 gene and initial characterization of its promoters. Li, Jiaqi,Wang, Liangliang,Zhang, Hao,Chen, Songling,Mei, Yingjie,Wang, Chong,Ling, Fei,Du, HongLi,Fang, Wei,Chen, Yaosheng,Liu, Xiaohui. 2010

作者其他论文 更多>>

微信小程序