Prediction of VIGS efficiency by the Sfold program and its reliability analysis in Gossypium hirsutum

文献类型： 外文期刊

第一作者： Xiaoyang Ge;;Jie Wu;;Chaojun Zhang

作者： Xiaoyang Ge;Jie Wu;Chaojun Zhang;Qianhua Wang;Yuxia Hou;Zuoren Yang;Zhaoen Yang;Zhenzhen Xu;Ye Wang;Lili Lu;Xueyan Zhang;Jinping Hua;Fuguang Li

作者机构：

关键词： VIGS;Sfold program;siRNA;Target sequences;Gossypium hirsutum

期刊名称：SCIENCE BULLETIN （ 影响因子：11.78； 五年影响因子：7.658 ）

ISSN： 2095-9273

年卷期： 2016 年 61 卷 7 期

页码：

收录情况： SCI

摘要： Genetic transformation in some plant species, including cotton (Gossypium hirsutum), is hampered by laborious and time-consuming processes and often unachievable. Virus-induced gene silencing (VIGS) by double-stranded RNAs can serve as a reverse-genetics tool to determine gene function. However, knockdown levels vary greatly when using a tobacco rattle virus-based vector that carries different cDNA fragments of a gene. How to choose the optional target fragment for high interference efficiency is very challenging. Addressing this challenge requires increasing the efficacy of small interference RNA (siRNA) in target fragment. Here, we describe a method to assess VIGS efficiency by comparing the following parameters of siRNA in target sequence: the disruption energy of the target (Delta G(disruption)), the differential stability of siRNA duplex ends (DSSE), and the internal stability at positions 9-14 of the siRNA antisense strand (AIS), which are calculated by Sfold program (http://sfold. wadsworth.org). We find that the siRNAs with low DGdisruption, high DSSE and high AIS have high activity and easily result in high VIGS efficiency by experimentally testing the actual knockdown levels of the four target genes, GhPDS, GhCLA1, GhAOS1, and GhCXE1 via choosing different target sequences for each gene. Therefore, the Sfold program can be used to analyze target sequences when carrying out VIGS design to increase gene-silencing effects in plants.

分类号：

  • 相关文献

[1]Molecular characterisation and functional analysis of a cytochrome P450 gene in cotton. Zhou, Kexue,Long, Lu,Sun, Quan,Wang, Weina,Gao, Wei,Cai, Chaowei,Mo, Jianchuan,Cheng, Jieru,Zhang, Xiangrui,Liu, Yujia,Miao, Chen,Zhang, Xiao,Cai, Yingfan,Du, Xiongming,Shi, Yuzhen,Yuan, Youlu,Chu, Zongyan.

[2]Characterization, Expression, and Functional Analysis of a Novel NAC Gene Associated with Resistance to Verticillium Wilt and Abiotic Stress in Cotton. Wang, Weina,Geng, Shuaipeng,Sun, Quan,Long, Lu,Cai, Chaowei,Liu, Xin,Wang, Guanghao,Miao, Chen,Zhang, Xiao,Cai, Yingfan,Wang, Weina,Yang, Can,Yuan, Youlu,Du, Xiongming,Chu, Zongyan. 2016

[3]A Novel AP2/ERF Transcription Factor CR1 Regulates the Accumulation of Vindoline and Serpentine in Catharanthus roseus. Gao, Fangyuan,Ren, Juansheng,Lu, Xianjun,Ren, Guangjun,Wang, Rui. 2017

[4]Two Lysin-Motif Receptor Kinases, Gh-LYK1 and Gh-LYK2, Contribute to Resistance against Verticillium wilt in Upland Cotton. Li, Fangfang,Qian, Shasha,Zhou, Xueping,Gu, Zhouhang,Wang, Qian,Ye, Fei,Liu, Tingli,Chen, Tianzi,Yang, Yuwen,Wang, Jinyan,Zhang, Baolong,Ding, Bo,Wang, Guoliang,Zhou, Xueping. 2017

[5]Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum). Wang, Jinyan,Hu, Zhongze,Zhao, Tongmin,Yang, Yuwen,Chen, Tianzi,Yang, Mali,Yu, Wengui,Zhang, Baolong. 2015

[6]PaCYP78A9, a Cytochrome P450, Regulates Fruit Size in Sweet Cherry (Prunus avium L.). Qi, Xiliang,Liu, Congli,Song, Lulu,Li, Yuhong,Li, Ming. 2017

[7]Identification of Putative Genes Involved in Limonoids Biosynthesis in Citrus by Comparative Transcriptomic Analysis. Wang, Fusheng,Liu, Xiaona,Xu, Yuanyuan,Zhu, Shiping,Shen, Wanxia,Zhao, Xiaochun,Wang, Fusheng,Liu, Xiaona,Xu, Yuanyuan,Zhu, Shiping,Shen, Wanxia,Zhao, Xiaochun,Wang, Fusheng,Zhu, Shiping,Shen, Wanxia,Zhao, Xiaochun,Wang, Fusheng,Wang, Mei. 2017

[8]Cotton Leaf Curl Multan Virus-Derived Viral Small RNAs Can Target Cotton Genes to Promote Viral Infection. Yang, Yuwen,Ma, Na,Ling, Xitie,Kan, Jialiang,Zhang, Baolong,Tang, Yafei,He, Zifu. 2016

[9]Silencing of NbXrn4 facilitates the systemic infection of Tobacco mosaic virus in Nicotiana benthamiana. Yan, Fei,Lu, Yuwen,Lin, Lin,Zheng, Hongying,Chen, Jianping,Yan, Fei,Lu, Yuwen,Lin, Lin,Zheng, Hongying,Chen, Jianping,Peng, Jiejun,Chen, Hairu,Yang, Jian,Jiang, Shanshan. 2011

[10]Molecular cloning and characterization of enhanced disease susceptibility 1 (EDS1) from Gossypium barbadense. Su, Xiaofeng,Qi, Xiliang,Cheng, Hongmei.

[11]Virus-induced silencing of a tobacco deoxyhypusine synthase gene. Wang, HZ,Ma, RC,Li, RF,Wang, GY,Wei, JH.

[12]Interference of porcine reproductive and respiratory syndrome virus replication on MARC-145 cells using DNA-based short interfering RNAs. He, Yun-xia,Hua, Rong-hong,Zhou, Yan-jun,Qiu, Hua-ji,Tong, Guang-zhi. 2007

[13]Expression of IL-13R alpha 2 in liver cancer cells and its effect on targeted therapy of liver cancer. Hou, Lingling,Du, Juan,Liu, Yanfeng,Sun, Weimin,Zheng, Yanpeng,Zhang, Lishu,Hu, Honggang,Dai, Xinxian,Hong, Tao,Wang, Jianwei,Guan, Weijun,Ma, Yuehui. 2010

[14]Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Wei, Bo,Zhang, Rongzhi,Li, Aili,Jia, Jizeng,Mao, Long,Wei, Bo,Zhang, Rongzhi,Li, Aili,Jia, Jizeng,Mao, Long,Cai, Tao,Li, Shan,Qi, Yijun,Huo, Naxin,Gu, Yong Q.,Vogel, John.

[15]Staphylococcus aureus infection of intestinal epithelial cells induces human umbilical cord-derived mesenchymal stem cell migration. Li, Yang,Liu, Ming-yuan,Wang, Xue-lin,Han, Wen-yu,Liu, Ya-hui,Suo, Jian,Li, Zhi-jie,Li, Ya-gang,Jin, Hu. 2013

[16]Effect of BMPRIB gene silencing by siRNA on apoptosis and steroidogenesis of porcine granulosa cells. Zhao, Y. Y.,Li, X. X.,Chen, X.,Yu, P.,Wang, J. J.,Xu, Y. X.,Wang, W.. 2014

[17]Cloning and RNA interference analysis of the salivary protein C002 gene in Schizaphis graminum. Fan Jia,Sun Jing-rui,Chen Ju-lian. 2015

[18]Construction of a genomewide RNAi mutant library in rice. Wang, Lei,Zheng, Jie,Luo, Yanzhong,Xu, Tao,Zhang, Qiuxue,Zhang, Lan,Xu, Miaoyun,Zhang, Chunyi,Fan, Yunliu,Wan, Jianmin,Wang, Ming-Bo. 2013

[19]Co-silence of the coatomer beta and v-ATPase A genes by siRNA feeding reduces larval survival rate and weight gain of cotton bollworm, Helicoverpa armigera. Zeng, Fanrong,Zhang, Peizhuo,Liu, Changyan.

[20]Study on the RNA interference of Sry in mouse embryos. Zhao Jin-Hong,Du Wei-Hua,Dao Er-Ji,Pei Jie,Zhang Li,Lin Xiu-Kun. 2006

作者其他论文 更多>>

微信小程序