The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa

文献类型： 外文期刊

第一作者： Subramaniam, Sabarinath

作者： Subramaniam, Sabarinath;Freeling, Michael;Wang, Xiaowu;Pires, J. Chris

作者机构：

关键词： conserved noncoding sequence;CNS;fractionation;mutagenesis;deletion;G-box;PIL5;Arabidopsis;Brassica rapa

期刊名称：GENOME BIOLOGY AND EVOLUTION （ 影响因子：3.416； 五年影响因子：4.079 ）

ISSN： 1759-6653

年卷期： 2013 年 5 卷 4 期

页码：

收录情况： SCI

摘要： Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana-A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with "deletion" in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a "deletion machine" in the Brassica lineage.

分类号：

  • 相关文献

[1]Genome Editing in Cotton with the CRISPR/Cas9 System. Wei Gao,Lu Long,Song, Chunpeng,Xinquan Tian,Ji Liu,Prashant K. Singh,Jose R. Botella,Chunpeng Song. 2017

[2]A fractionation procedure for identifying novel proteins induced by chill stress in Arabidopsis thaliana. Sun, Liwen,Wang, Shichen,Yang, Shuo,Liu, Xiangguo,Chai, Xin,Xin, Hongbao,An, Baiyi,Hao, Dongyun,Xi, Jinghui.

[3]Biotoxicity of Cry1Ab protein on wolf spider Pardosa pseudoannulata. Wang, Juan,Yang, Huilin,Yan, Zhenzhen,Li, Qinjin,Shi, Yixue,Liang, Yunshan,Wang, Zhi,Peng, Yuande,Xie, Chunliang,Song, Qisheng.

[4]New cis-regulatory elements in the Rht-D1b locus region of wheat. Duan, Jialei,Wu, Jiajie,Liu, Yue,Xiao, Jianhui,Zhao, Guangyao,Jia, Jizeng,Kong, Xiuying,Gu, Yongqiang,Duan, Jialei. 2012

[5]High-Purity Calycosin-7-O--D-glucopyranoside Recovered from Radix Astragali by Extraction, Fractionation and Recrystallization. Shi, Bo,Xiao, Wei-hua,Han, Lu-jia. 2009

[6]Antitumor activity of bee pollen polysaccharides from Rosa rugosa. Wang, Bo,Zhang, Zhongyu,Liu, Yang,Gao, Qipin,Zhou, Yifa,Li, Shanshan,Diao, Qiyu.

[7]Fractionation, partial characterization and bioactivity of water-soluble polysaccharides and polysaccharide-protein complexes from Pleurotus geesteranus. Zhang, Mei,Zhu, Lin,Cui, Steve W.,Wang, Qi,Zhou, Ting,Shen, Hengsheng.

[8]Ageing of added copper in bentonite without and with humic acid. Zhou, Shi-Wei,Ma, Yi-Bing,Xu, Ming-Gang,Zhou, Shi-Wei.

[9]Is soil dressing a way once and for all in remediation of arsenic contaminated soils? A case study of arsenic re-accumulation in soils remediated by soil dressing in Hunan Province, China. Su, Shiming,Bai, Lingyu,Gao, Xiang,Zhang, Tuo,Wang, Yanan,Li, Lianfang,Wang, Jinjin,Wu, Cuixia,Zeng, Xibai,Wei, Caibing.

[10]Comparative Analysis of Polysaccharides from Two Ecological Types of Leymus chinensis. Bi Hong-tao,Li Jing-jing,Chen Xi-guang,Yan Ji-hong,Sun Fang,Fan Sha-sha,Cao Gang,Zhou Yi-fa. 2012

[11]Comparison of anti-browning ability and characteristics of the fractionated Maillard reaction products with different polarities. Yuan, Debao,Xu, Yinghao,Wang, Chaozheng,Li, Yixing,Li, Fenfang,Zhou, Ya,Chen, Jiao,Jin, Zhiqiang,Zhang, Haide,Jiang, Yueming.

[12]Fractionation of corn stover into cellulose, hemicellulose and lignin using a series of ionic liquids. Zhang, Peng,Ma, Hui-Hui,Wang, Yu-Fei,Hu, Xiao-Mei,Dong, Shi-Jia,Zhang, Bi-Xian.

[13]Metals in exposed-lawn soils from 18 urban parks and its human health implications in southern China's largest city, Guangzhou. Gu, Yang-Guang,Lin, Qin,Gu, Yang-Guang,Lin, Qin,Gu, Yang-Guang,Lin, Qin,Gao, Yan-Peng,Gao, Yan-Peng.

[14]Genome shuffling of Lactobacillus plantarum C88 improves adhesion. Zhao, Yujuan,Duan, Cuicui,Gao, Lei,Yu, Xue,Niu, Chunhua,Li, Shengyu. 2017

[15]Molecular biological effect of (CO)-C-60 gamma-ray irradiation on rice genome DNA. Xiang, TH,Yang, JB,Yang, QJ,Zhu, QS,Li, L,Ni, DH,Wang, XF,Huang, DN. 2002

[16]The pqqC gene is essential for antifungal activity of Pseudomonas kilonensis JX22 against Fusarium oxysporum f. sp lycopersici. Xu, Jianhong,Xu, Jianhong,Deng, Peng,Baird, Sonya M.,Lu, Shi-En,Showmaker, Kurt C.,Wang, Hui. 2014

[17]Structural and biochemical insights into the degradation mechanism of chitosan by chitosanase OU01. Lyu, Qianqian,Yang, Yan,Han, Baoqin,Liu, Wanshun,Liu, Weizhi,Shi, Yanhong,Wang, Song,Jones, David N. M..

[18]Insights into the roles of non-catalytic residues in the active site of a GH10 xylanase with activity on cellulose. Chu, Yindi,Tu, Tao,Xue, Xianli,Wang, Xiaoyu,Gong, Li,Luo, Huiying,Yao, Bin,Su, Xiaoyun,Penttinen, Leena,Rouvinen, Juha,Hakulinen, Nina,Yi, Zhuolin,Gong, Li. 2017

[19]Generation of peanut mutants by fast neutron irradiation combined with in vitro culture. Wang, Jing-Shan,Sui, Jiong-Ming,Qiao, Li-Xian,Xie, Yong-Dun,Guo, Hui-Jun,Liu, Lu-Xiang,Zhao, Li-Lan,Yu, Shan-Lin. 2015

[20]A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences. Xiong, Ai-Sheng,Peng, Ri-He,Zhuang, Jing,Liu, Jin-Ge,Gao, Feng,Xu, Fang,Cai, Bin,Yao, Quan-Hong.

作者其他论文 更多>>

微信小程序