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Next generation sequencing brings a new life of“GWA”study

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Next generation sequencing brings a new life of“GWA”study

Overexpression of a tobacco small G protein gene NtRop1 causes salt sensitivity and hydrogen peroxide production in transgenic plants

第八次全国医学遗传学学术会议(中华医学会2009年医学遗传学年会)

作者： Wang Jun,Zhang Yong,Yang Xu beijing genomics institute- Shenzhen

Drawing genetic risk profiles using genome wide association studies(GWA)is applied hot by so many scientists recent *** powerful tool is HapMap and Chips(From 550K to 1M chip).The GWA study race in obesity,type 2 diabetes,hypertension and other complex traits started about 2-3.years ago,and so many papers have recently been *** the first GWA race, it is the time for *** on the Shortcomings of the HapMap concept and current chip based technology:rare gene variants, many of which may contribute with a high relative risk to obesity,type 2 diabetes,hypertension and other complex traits are not cap- *** is the time to skip the HapMap concept and concentrate on whole genome sequencing.A denser SNP mapping is needed in the second generation GWA studies and in the post-GWA era high-capacity whole-genome sequencing technology like Solexa is needed. The Three-dimensional translational genomics research space can be divided as clinical data,genome breath and the *** Ideal Research should include Over 10,000 samples,Whole genome sequencing and Best gene annotation and phenotypic information,this is the direction of our efforts and we need your cooperation.

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Science China(Life Sciences) 2008年第5期51卷 383-390页

作者： CAO YangRong1,2, LI ZhiGang1,2, CHEN Tao1,2, ZHANG ZhiGang1, ZHANG JinSong1 & CHEN ShouYi1 1 National Key Lab of Plant genomics, institute of Genetics and Developmental Biology, Chinese Academy of Sciences, beijing 100101, China 2 Graduate School of Chinese Academy of Sciences, beijing 10003., China National Key Lab of Plant genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China Graduate School of Chinese Academy of Sciences Beijing China

The small GTPases of Rop/Rho family is central regulators of important cellular processes in plants. Tobacco small G protein gene NtRop1 has been isolated; however, its roles in stress responses were unknown. In the present study, the genomic sequence of NtRop1 was cloned, which has seven exons and six introns, similar to the Rop gene structure from Arabidopsis. The NtRop1 gene was constitutively expressed in the different organs whereas the other six Rop genes from tobacco had differential expression patterns. The expression of the NtRop1 gene was moderately induced by methyl viologen, NaCl, and ACC treatments, but slightly inhibited by ABA treatment, with no significant induction by NAA treatment. The transgenic Arabidopsis plants overexpressing the NtRop1 showed increased salt sensitivity as can be seen from the reduced root growth and elevated relative electrolyte leakage. The hydrogen peroxide production was also promoted in the NtRop1-trangenic plants in comparison with wild type plants. These results imply that the NtRop1 may confer salt sensitivity through activation of H2O2 production during plant response to salt stress.

关键词： small G protein NtRop1 salt sensitive hydrogen peroxide

DNA sequence comparative analysis of the 3.ter-p26 region of human genome

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Science China(Life Sciences) 2005年第1期48卷 34-40页

作者： LUO Chunqing, LI Yan, ZHANG Xiaowei, ZHANG Yilin, ZHANG Haiqing, CHEN Chong, XU Zuyuan, CUI Peng, HU Songnian, YANG Huanming & DONG Wei institute of Genetic and Developmental Biology, Chinese Academy of Sciences, beijing 100101, China beijing {3. institute, Chinese Academy of Sciences, beijing 1013.0, China institute of Genetic and Developmental Biology Chinese Academy of Sciences Beijing100101China beijing genomics institute Chinese Academy of Sciences Beijing101300 China beijing genomics institute Chinese Academy of Sciences Beijing101300 China

Most proterminal regions of human chromosomes are GC-rich and gene-rich. Chromosome 3. is an exception. Its proterminal region is GC-poor, and likely to lose heterozygosity, thus causing a number of fatal diseases. Except one gap left in the telomeric position, the proterminal region of human chromosome 3. has been completely sequenced. The detailed sequence analysis showed: (i) the GC content of this region was 3..5%, being the lowest among all the human proterminal regions; (ii) this region contained 20 known genes and 22 predicted genes, with an average gene size of 97.5 kb. The previously mapped gene Cntn3.was not found in this region, but instead located in the 74 Mb position of human chromosome 3.; (iii) the interspersed repeats of this region were more active than the average level of the whole human genome, especially (TA)n, the content of which was twice the genome average; (iv) this region had a conserved synteny extending from 104.1 Mb to 112.4 Mb on the mouse chromosome 6, which was 8% larger in size, not in accordance with the whole genome comparison, probably because the 3.ter-p26 region was more likely to lose neocleitides and its mouse synteny had more active interspersed repeats.

关键词： comparative analysis, 3.ter-p26, human genome.

生物信息学在新基因全长cDNA序列分析及功能预测中的应用

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生物化学与生物物理进展 2003年第1期30卷 159-163页

作者：张成岗贺福初军事医学科学院放射医学研究所北京100850

差异表达基因的检测与分析已成为研究具有差异的生物学表型的常规策略 .对通过实验所获得的差异基因片段进行生物信息学分析 ,主要包括基于国际互联网的序列相似性分析、片段重叠群分析和全长cDNA序列分析 ,以及如何构建局域网并采用本... 详细信息

差异表达基因的检测与分析已成为研究具有差异的生物学表型的常规策略 .对通过实验所获得的差异基因片段进行生物信息学分析 ,主要包括基于国际互联网的序列相似性分析、片段重叠群分析和全长cDNA序列分析 ,以及如何构建局域网并采用本地服务器进行规模化的数据分析 ,从而为研究人员提供可参考的生物信息学数据分析方案 .

关键词：生物信息学全长cDNA序列分析功能预测 PC机数据分析新基因

Genomic Sequence and Analysis of Miscanthus lutarioriparia,a Promising Bioenergy Crop in Middle China

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Genomic Sequence and Analysis of Miscanthus lutarioriparia,a...

Genomic and genic sequence variation in synthetic hexaploid wheat (AABBDD) as compared to their parental species

第十二届全国植物基因组学大会

作者： Ying Lu~1,Qiang Zhao~1,Qi Feng~1,Tingting Lu~1,Tao Sang~(1,2),Bin Han~(1,3. 1.National Centre for Gene Research &institute of Plant Physiology and Ecology,Shanghai institute for Biological Sciences, Chinese Academy of Sciences,500 Caobao Road,Shanghai 20023.,China 2.Department of Plant Biology,Michigan State University, East Lansing,Michigan 48824,USA 3.beijing institute of genomics,Chinese Academy of Sciences,7 Beitucheng West Road,beijing 100029,China

Miscanthus is a genus of woody,perennial,tufted rhizomatous grasses originated in East *** many species of it has been identified as potential energy crops,there is little information on genomic sequence, gene expression,and comparative *** lutarioriparia(firstly named as Triarrbena lutariorparia) is one of the tallest species and grows in Middle *** has high potential of biomass productivity and could be used as a source of renewable raw material and energy. *** is a member of the grass family *** did the genome sequence by whole

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Progress in Natural Science:Materials International 2008年第5期18卷 533-538页

作者： Lihong Nie, Zongfu Han, Lahu Lu, Yingyin Yao, Qixin Sun, Zhongfu Ni Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop genomics and Genetic Improvement (MOA), beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics & Breeding, China Agricultural University, beijing 100094, China Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Genomics and Genetic Improvement (MOA) Beijing Key Laboratory of Crop Genetic Improvement Department of Plant Genetics & Breeding China Agricultural University Beijing 100094 China

In order to understand the genomic changes during the evolution of hexaploid wheat, two sets of synthetic hexaploid wheat from hybridization between maternal tetraploid wheat (AABB) and paternal diploid goat grass (DD) were used for DNA-AFLP and single strand conformation polymorphism (SSCP) analysis to determine the genomic and genic variation in the synthetic hexaploid wheat. Results indicated that more DNA sequences from paternal diploid species were eliminated in the synthetic hexaploid wheat than from maternal tetraploid wheat, suggesting that genome from parental species of lower ploidity tends to be eliminated preferentially. However, sequence variation detected by SSCP procedure was much lower than those detected by DNA-AFLP, which indicated that much less variation in the genic regions occurred in the synthetic hexaploid wheat, and sequence variations detected by DNA-AFLP could be derived mostly from non-coding regions and repetitive sequences. Our results also indicated that sequence variation in 4 genes can be detected in hybrid F1, which suggested that this type of sequence variation could be resulted from distant hybridization. It was interesting to note that 3.out of the 4 genes were mapped and clustered on the long arm of chromosome 2D, which indicated that variation in genic sequences in synthetic hexaploid wheat might not be a randomized process.

关键词： Synthetic hexaploid wheat Polyploidy Genome Sequence variation

A draft sequence of the rice (Oryza sativa ssp. indica) genome

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Chinese Science Bulletin 2001年第23期46卷 1937-1942页

作者： YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG Huanmingbeijing genomics institute/Center of genomics & Bioinformatics, Chinese Academy of Sciences, beijing 1013.0, China Hangzhou genomics institute/institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 3.0007, China institute of Genetics, Chinese Academy of Sciences, beijing 100101, China National Hybrid Rice R & D Center, Changsha 410125, China Laboratory of Bioinformatics, institute of Biophysics, Chinese Academy of Sciences, beijing 100101, China College of Life Sciences, Peking University, beijing 100871, China institute of Theoretical Physics, Chinese Academy of Sciences, beijing 1Q0080, China Digital China Ltd., beijing 100080, China institute of Computing Technology, Chinese Academy of Sciences, beijing 100080, China Medical College, Xi’an Jiaotong University, Xi’an 710061, ChinaThese authors contributed equally to this work.Corresponding author.Corresponden beijing genomics institute/Center of genomics & Bioinformatics Chinese Academy of Sciences Beijing China Hangzhou genomics institute/institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province Hangzhou China College of Life Sciences Peking University Beijing China Medical College Xi’an Jiaotong University Xi’an China institute of Genetics Chinese Academy of Sciences Beijing China Laboratory of Bioinformatics Institute of Biophysics Chinese Academy of Sciences Beijing China National Hybrid Rice R & D Center Changsha China institute of Theoretical Physics Chinese Academy of Sciences Beijing China Digital China Ltd. Beijing China institute of Computing Technology Chinese Academy of Sciences Beijing China

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3.million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.3. million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93.11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package

关键词： rice genome draft sequences.

Shotgun法测序制备高纯度水稻基因组DNA的方法探讨(英文)

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生物化学与生物物理进展 2003年第5期30卷 744-748页

作者：杨继良王辉王庆华李军刘斌金德敏王斌中国科学院遗传与发育生物学研究所北京100101 中国科学院北京基因组学研究所北京101300 山东大学生命科学院济南250100

在用散弹 (shotgun)法测定水稻 (OryzasativaL .ssp .indica)基因组全序列的过程中 ,叶绿体和线粒体DNA的污染问题非常严峻 .应用脉冲场电泳 (PFGE)技术对水稻基因组DNA进行纯化 ,结果表明它能够有效去除叶绿体和线粒体DNA ,使其污染率... 详细信息

在用散弹 (shotgun)法测定水稻 (OryzasativaL .ssp .indica)基因组全序列的过程中 ,叶绿体和线粒体DNA的污染问题非常严峻 .应用脉冲场电泳 (PFGE)技术对水稻基因组DNA进行纯化 ,结果表明它能够有效去除叶绿体和线粒体DNA ,使其污染率从 3.降低到 0 2 % .同时 ,比较了水稻绿苗和黄化苗的DNA得率 ,以及HB法和NIB法制备大分子质量(HMW)DNA的异同 .最后提出一套制备水稻基因组DNA的方法 ,包括黄化苗培养 ;细胞核的分离、包埋和裂解 ;脉冲场电泳纯化、回收聚集在低熔点 (LMP)胶中的水稻HMWDNA .用该方法所得的水稻基因组DNA ,纯度高 (无叶绿体和线粒体DNA污染 )、基因组完整 (机械剪切和降解少 )、回收率高 (操作过程中DNA损失少 ) .另外 ,首次报道在融化的低熔点(LMP)胶中对水稻HMWDNA于 3.℃进行超声波处理 ,能够获得用于shotgun文库和梯度文库构建所需要的各种DNA片段(1 5～ 3.b ,3. 12kb) 。

关键词： Shotgun法测序水稻基因组DNA 纯化

Jackknife and Bootstrap Tests of the Composition Vector Trees

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genomics, Proteomics & Bioinformatics 2010年第4期8卷 262-267页

作者： Guanghong Zuo1,2, Zhao Xu1,3. Hongjie Yu1,4, and Bailin Hao1,5,6 1T-Life Research Center & Department of Physics, Fudan University, Shanghai 20043., China 2Shanghai institute of Applied Physics, Chinese Acadamy of Sciences, Shanghai 201800, China 3.pplied Biosystems, Inc., beijing 100027, China 4Fudan-VARI Center for Genetic Epidemiology, Fudan University, Shanghai 20043., China 5institute of Theoretical Physics, Chinese Acadamy of Sciences, beijing 100190, China 6Santa Fe institute, Santa Fe, NM 87505, USA. T-Life Research Center & Department of Physics Fudan University Shanghai 200433 China.

Composition vector trees （CVTrees） are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.

关键词： composition vector phylogeny topological distance bootstrap jackknife CVTree