Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet

文献类型： 外文期刊

第一作者： Wang, Yongqiang

作者： Wang, Yongqiang;Li, Lin;Diao, Xianmin;Tang, Sha;Zhi, Hui;Jia, Guanqing;Diao, Xianmin;Wang, Yongqiang;Liu, Jianguang;Zhang, Hanshuang

作者机构：

关键词： miRNA;High-throughput sequencing;Drought;Foxtail millet;Degradome

期刊名称：BMC GENETICS （ 影响因子：2.797； 五年影响因子：3.263 ）

ISSN： 1471-2156

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: Foxtail millet (Setaria italica) is a diploid C-4 panicoid species. Because of its prominent drought resistance, small genome size, self-pollination, and short life cycle, foxtail millet has become an ideal model system for studying drought tolerance of crops. MicroRNAs (miRNAs) are endogenous, small RNAs that play important regulatory roles in the development and stress response in plants. Results: In this study, we applied Illumina sequencing to systematically investigate the drought-responsive miRNAs derived from S. italica inbred An04-4783 seedlings grown under control and drought conditions. Degradome sequencing was applied to confirm the targets of these miRNAs at a global level. A total of 81 known miRNAs belonging to 28 families were identified, among which 14 miRNAs were upregulated and four were downregulated in response to drought. In addition, 72 potential novel miRNAs were identified, three of which were differentially expressed under drought conditions. Degradome sequencing analysis showed that 56 and 26 genes were identified as targets of known and novel miRNAs, respectively. Conclusions: Our analysis revealed post-transcriptional remodeling of cell development, transcription factors, ABA signaling, and cellar homeostasis in S. italica in response to drought. This preliminary characterization provided useful information for further studies on the regulatory networks of drought-responsive miRNAs in foxtail millet.

分类号：

  • 相关文献

[1]Small RNA and Degradome Deep Sequencing Reveals Peanut MicroRNA Roles in Response to Pathogen Infection. Zhao, Chuanzhi,Xia, Han,Zhao, Shuzhen,Hou, Lei,Zhang, Ye,Li, Changsheng,Wang, Xingjun,Zhao, Chuanzhi,Xia, Han,Zhao, Shuzhen,Hou, Lei,Zhang, Ye,Li, Changsheng,Wang, Xingjun,Cao, Tingjie,Zhang, Xinyou,Yang, Yu.

[2]Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize. Zhao, Yongping,Xu, Zhenhua,Mo, Qiaocheng,Zou, Cheng,Li, Wenxue,Xu, Yunbi,Xie, Chuanxiao,Xu, Yunbi,Mo, Qiaocheng,Xu, Zhenhua.

[3]Dual transcriptome analysis reveals insights into the response to Rice black-streaked dwarf virus in maize. Zhou, Yu,Duan, Canxing,Hao, Zhuanfang,Li, Mingshun,Yong, Hongjun,Zhang, Degui,Zhang, Shihuang,Weng, Jianfeng,Li, Xinhai,Zhou, Yu,Xu, Zhennan,Wang, Zhenhua,Chen, Yanping,Meng, Qingchang,Wu, Jirong.

[4]Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication. Wang, Yu,Bai, Xuefei,Yan, Chenghai,Gui, Yiejie,Fan, Longjiang,Wang, Yu,Bai, Xuefei,Yan, Chenghai,Gui, Yiejie,Fan, Longjiang,Wei, Xinghua,Guo, Longbiao,Zhu, Qian-Hao.

[5]Overexpression of the autophagy-related gene SiATG8a from foxtail millet (Setaria italica L.) confers tolerance to both nitrogen starvation and drought stress in Arabidopsis. Li, Wei-wei,Liu, Jia-ming,Guo, Chang-Hong,Chen, Ming,Xu, Zhao-shi,Li, Lian-cheng,Zhou, Yong-Bin,Ma, You-Zhi,Zhong, Li.

[6]Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development. Gao, Chao,Wang, Pengfei,Zhao, Shuzhen,Zhao, Chuanzhi,Xia, Han,Hou, Lei,Zhang, Ye,Li, Changsheng,Wang, Xingjun,Wang, Xingjun,Ju, Zheng. 2017

[7]Identification and characterization of Cynoglossus semilaevis microRNA response to Vibrio anguillarum infection through high-throughput sequencing. Sha, Zhenxia,Gong, Guangye,Lu, Yang,Wang, Lei,Chen, Songlin,Gong, Guangye,Lu, Yang,Wang, Shaolin,Wang, Qilong.

[8]Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana. Yin, Kangquan,Tang, Yang,Zhao, Jinping,Zhao, Jinping. 2015

[9]Conserved miRNAs and Their Response to Salt Stress in Wild Eggplant Solanum linnaeanum Roots. Zhuang, Yong,Zhou, Xiao-Hui,Liu, Jun. 2014

[10]Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing. Bi, Fangcheng,Meng, Xiangchun,Yi, Ganjun,Bi, Fangcheng,Meng, Xiangchun,Yi, Ganjun,Bi, Fangcheng,Meng, Xiangchun,Yi, Ganjun,Ma, Chao. 2015

[11]MicroRNAs associated with drought response in the pulse crop common bean (Phaseolus vulgaris L.). Wu, Jing,Wang, Lanfen,Wang, Shumin. 2017

[12]Arabidopsis enhanced drought tolerance1/HOMEODOMAIN GLABROUS11 confers drought tolerance in transgenic rice without yield penalty. Yu, Linhui,Chen, Xi,Wang, Zhen,Xiang, Chengbin,Wang, Shimei,Zhu, Qisheng,Wang, Yuping,Li, Shigui,Wang, Shimei,Zhu, Qisheng.

[13]Characterization and function of Tomato yellow leaf curl virus-derived small RNAs generated in tolerant and susceptible tomato varieties. Bai Miao,Yang Guo-shun,Chen Wen-ting,Lin Run-mao,Ling Jiang,Mao Zhen-chuan,Xie Bing-yang. 2016

[14]Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches. Shi, Mengya,Hu, Xiao,Shi, Mengya,Wei, Yu,Liu, Jun,Hou, Xu,Yuan, Xue,Liu, Yueping,Liu, Yueping. 2017

[15]Analyses of a Glycine max Degradome Library Identify microRNA Targets and MicroRNAs that Trigger Secondary SiRNA Biogenesis. Hu, Zheng,Jiang, Qiyan,Ni, Zhiyong,Xu, Shuo,Zhang, Hui,Chen, Rui. 2013

[16]Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses. Yu, Ying,Yuan, Hongmei,Guan, Fengzhi,Yu, Ying,Wu, Guangwen,Yuan, Hongmei,Cheng, Lili,Zhao, Dongsheng,Huang, Wengong,Zhang, Shuquan,Zhang, Liguo,Guan, Fengzhi,Chen, Hongyu,Zhang, Jian. 2016

[17]Response of microRNAs to cold treatment in the young spikes of common wheat. Song, Guoqi,Zhang, Rongzhi,Zhang, Shujuan,Li, Yulian,Gao, Jie,Han, Xiaodong,Chen, Mingli,Wang, Jiao,Li, Wei,Li, Genying,Song, Guoqi,Zhang, Rongzhi,Zhang, Shujuan,Li, Yulian,Gao, Jie,Han, Xiaodong,Chen, Mingli,Wang, Jiao,Li, Wei,Li, Genying,Song, Guoqi,Zhang, Rongzhi,Zhang, Shujuan,Li, Yulian,Gao, Jie,Han, Xiaodong,Chen, Mingli,Wang, Jiao,Li, Wei,Li, Genying. 2017

[18]Genome-Wide Characterization of Rice Black Streaked Dwarf Virus-Responsive MicroRNAs in Rice Leaves and Roots by Small RNA and Degradome Sequencing. Sun, Zongtao,He, Yuqing,Li, Junmin,Wang, Xu,Chen, Jianping,He, Yuqing.

[19]Effects of components in culture medium on glutamate decarboxylase activity and gamma-aminobutyric acid accumulation in foxtail millet (Setaria italica L.) during germination. Bai, Qingyun,Gu, Zhenxin,Cao, Xiaohong,Li, Yan,Liu, Kunlun,Bai, Qingyun,Chai, Meiqing. 2009

[20]Foxtail Millet CBL4 (SiCBL4) Interacts with SiCIPK24, Modulates Plant Salt Stress Tolerance. Zhang, Yumin,Linghu, Jingjing,Wang, Dong,Liu, Xi,Li, Fengting,Zhao, Tianyong,Zhang, Yumin,Linghu, Jingjing,Wang, Dong,Liu, Xi,Li, Fengting,Zhao, Tianyong,Zhang, Yumin,Linghu, Jingjing,Wang, Dong,Liu, Xi,Li, Fengting,Zhao, Tianyong,Yu, Aili,Zhao, Jinfeng. 2017

作者其他论文 更多>>

微信小程序