Identification of genes alternatively spliced in developing maize endosperm

文献类型： 外文期刊

第一作者： Xie, S.

作者： Xie, S.;Zhang, J.;Xie, S.;Zhang, X.;Zhou, Z.;Li, X.;Weng, J.;Huang, Y.

作者机构：

关键词： Alternative splicing;endosperm development;intron retention;maize;RNA sequencing

期刊名称：PLANT BIOLOGY （ 影响因子：3.081； 五年影响因子：2.972 ）

ISSN： 1435-8603

年卷期： 2018 年 20 卷 1 期

页码：

收录情况： SCI

摘要： The process of alternative splicing is critical for the regulation of growth and development of plants. Thus far, little is known about the role of alternative splicing in the regulation of maize (Zea mays L.) endosperm development. RNA sequencing (RNA-seq) data of endosperms from two maize inbred lines, Mo17 and Ji419, at 15 and 25days after pollination (DAP), respectively, were used to identify genes that were alternatively spliced during endosperm development. Intron retention (IR) in GRMZM2G005887 was further validated using PCR and re-sequencing technologies. In total, 49,000 alternatively spliced events and ca. 20,000 alternatively spliced genes were identified in the two maize inbred lines. Of these, 30 genes involved in amino acid biosynthesis and starch biosynthesis were identified, with IR occurring only in a specific sample, and were significantly co-expressed with ten well-known genes related to maize endosperm development. Moreover, IR in GRMZM2G005887, which encodes a cysteine synthase, was confirmed to occur only in the endosperm of Mo17 at 15 DAP, resulting in the retention of a 121-bp fragment in its 5 untranslated region. Two cis-acting regulatory elements, CAAT-box and TATA-box were observed in the retained fragment in Mo17 at 15 DAP; this could regulate the expression of this gene and influence endosperm development. The results suggest that the 30 genes with IR identified herein might be associated with maize endosperm development, and are likely to play important roles in the developing maize endosperm.

分类号：

  • 相关文献

[1]An Arabidopsis gene encoding a C2H2-domain protein with alternatively spliced transcripts is essential for endosperm development. Lu, Xiaoduo,Liang, Qiuju,Fan, Yunliu,Zhang, Chunyi,Lu, Xiaoduo,Li, Yuan,Su, Yanping,Shen, Songdong,Liang, Qiuju,Meng, Hongyan,Fan, Yunliu,Zhang, Chunyi,Li, Sha. 2012

[2]Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae. Jin, Lirong,Yu, Dazhao,Huang, Wei,Li, Guanglin,Cheng, Chao,Liao, Shengjie,Zhang, Yi,Liao, Shengjie,Wu, Qijia,Zhang, Yi,Li, Guanglin,Wu, Qijia. 2017

[3]Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms. Zhao, Zhixin,Wu, Xiaohui,Kumar, Praveen Kumar Raj,Dong, Min,Li, Qingshun Quinn,Liang, Chun,Wu, Xiaohui,Dong, Min,Ji, Guoli,Li, Qingshun Quinn,Li, Qingshun Quinn,Li, Qingshun Quinn. 2014

[4]Intron retention and 3 '-UTR analysis of Arabidopsis Dicer-like 2 transcripts. He, Qiongji,Peng, Jiejun,Yan, Fei,Lin, Lin,Lu, Yuwen,Zheng, Hongying,Chen, Jianping,He, Qiongji,Peng, Jiejun,Yan, Fei,Lin, Lin,Lu, Yuwen,Zheng, Hongying,Chen, Jianping,He, Qiongji,Peng, Jiejun,Chen, Hairu.

[5]The U6 Biogenesis-Like 1 Plays an Important Role in Maize Kernel and Seedling Development by Affecting the 3 ' End Processing of U6 snRNA. Li, Jiankun,Fu, Junjie,Chen, Yan,Fan, Kaijian,Li, Li,Liu, Yunjun,Zheng, Jun,Wang, Guoying,Li, Jiankun,Ren, Dongtao,He, Cheng,Zhang, Zhiqiang. 2017

[6]Comparative transcript profiling of maize inbreds in response to long-term phosphorus deficiency stress. Sun, Yanling,Mu, Chunhua,Zhang, Hui,Wang, Qingcheng,Xue, Yanfang,Li, Zongxin,Liu, Xia,Chen, Yu,Kong, Xiangpei,Zheng, Hongxia,Ding, Zhaojun,Liu, Xia,Xu, Yuanchao.

[7]Two alternative splicing variants of maize HKT1;1 confer salt tolerance in transgenic tobacco plants. Ren, Zhenjing,Kang, Dan,Fan, Kaijian,Wang, Cuiyun,Wang, Guoying,Liu, Yunjun,Liu, Yan.

[8]Analysis of sea-island cotton and upland cotton in response to Verticillium dahliae infection by RNA sequencing. Quan Sun,Huaizhong Jiang,Xiaoyan Zhu,Weina Wang,Xiaohong He,Yuzhen Shi,Youlu Yuan,Xiongming Du,Yingfan Cai. 2013

[9]Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis. Li, Tingting,Zhang, Genxi,Wu, Pengfei,Liu, Qiuhong,Wang, Jinyu,Duan, Lian,Li, Guohui. 2018

[10]An efficient and rapid method to detect and verify natural antisense transcripts of animal genes. Zhang Li,Zhao Rui,Xiao Mei,An Li-long,Lin Shu-dai,Li Bi-xiao,Qiu Feng-fang,Ma Jing-e,Zhang De-xiang,Nie Qing-hua,Zhang Xi-quan. 2016

[11]Whole genome re-sequencing and transcriptome analysis of the Stylosanthes Anthracnose pathogen Colletotrichum gloeosporioides reveal its characteristics. Huang, H. P.,Huang, H. P.,Huang, J. H.,Zheng, J. L.,Yi, K. X.,Ma, S.. 2016

[12]An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.). Ye, Jiang,Yang, Yuhua,Shi, Jiaqin,Zhan, Jiepeng,Wang, Xinfa,Liu, Guihua,Wang, Hanzhong,Chen, Bo,Luo, Meizhong. 2017

[13]Hepatic transcriptome analysis of juvenile GIFT tilapia (Oreochromis niloticus), fed diets supplemented with different concentrations of resveratrol. Zheng, Yao,Wu, Wei,Hu, Gengdong,Meng, Shunlong,Fan, Limin,Song, Chao,Qiu, Liping,Chen, Jiazhang,Zhao, Zhixiang,Chen, Jiazhang,Chen, Jiazhang. 2018

[14]Integrating Small RNA Sequencing with QTL Mapping for Identification of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice. Liu, Qing,Yang, Tifeng,Zhang, Shaohong,Mao, Xingxue,Zhao, Junliang,Wang, Xiaofei,Dong, Jingfang,Liu, Bin,Liu, Qing,Yang, Tifeng,Zhang, Shaohong,Mao, Xingxue,Zhao, Junliang,Wang, Xiaofei,Dong, Jingfang,Liu, Bin,Yu, Ting. 2017

[15]Comparative Transcriptome Analysis between Broccoli (Brassica oleracea var. italica) and Wild Cabbage(Brassica macrocarpa Guss.) in Response to Plasmodiophorabrassicae during Different Infection Stages. Zhang, Xiaoli,Liu, Yumei,Fang, Zhiyuan,Li, Zhansheng,Yang, Limei,Zhuang, Mu,Zhang, Yangyong,Lv, Honghao. 2016

[16]Comparative transcriptome analyses indicate enhanced cellular protection against FMDV in PK15 cells pretreated with IFN-gamma. Fu, Yin,Zhu, Zesen,Liu, Jing,Chen, Huiyong,Fu, Yin,Zhu, Zesen,Liu, Jing,Chen, Huiyong,Chang, Huiyun,Liu, Zaixin.

[17]Transcriptome analysis reveals translational regulation in barley microspore-derived embryogenic callus under salt stress. Liu, Cheng-hong,Lu, Rui-ju,Guo, Gui-mei,He, Ting,Li, Ying-bo,Xu, Hong-wei,Gao, Run-hong,Chen, Zhi-wei,Huang, Jian-hua,Liu, Cheng-hong,Lu, Rui-ju,Guo, Gui-mei,He, Ting,Li, Ying-bo,Xu, Hong-wei,Gao, Run-hong,Chen, Zhi-wei,Huang, Jian-hua.

[18]Analysis of differentially expressed genes and adaptive mechanisms of Prunus triloba Lindl. under alkaline stress. Wang, Yongqing,Liu, Jia,Liu, Jia,Li, Qingtian. 2017

[19]Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress. Huang, Liyu,Zhang, Fan,Zhang, Fan,Wang, Wensheng,Zhou, Yongli,Fu, Binying,Li, Zhikang,Zhang, Fan. 2014

[20]Transcriptome analysis reveals novel genes involved in anthocyanin biosynthesis in the flesh of peach. Cao, Ke,Ding, Tiyu,Mao, Dongmin,Zhu, Gengrui,Fang, Weichao,Chen, Changwen,Wang, Xinwei,Wang, Lirong. 2018

作者其他论文 更多>>

微信小程序