|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | Molecular phylogeny of coronaviruses including human SARS-CoV显示文摘Phylogenetic tree of coronaviruses (CoVs) in-cluding the human SARS-associated virus is reconstructed from complete genomes by using our newly developed K- string composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup. SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus ge-nomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV. | GAO Lei QI Ji WEI Haibin SUN Yigang HAO Bailin | 2003 | Chinese Science Bulletin2003，48，12： | 7 |
| 2 | A draft sequence of the rice (Oryza sativa ssp. indica) genome显示文摘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 3.30 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 | 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 101300, China Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, 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 | 2001 | Chinese Science Bulletin2001，46，23： | 6 |
| 3 | The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize显示文摘Southern corn rust(SCR),caused by the fungal pathogen Puccinia polysora,is a major threat to maize pro-duction worldwide.Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR.Here,we report the molecular cloning and characterization of RppC,which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus.Further-more,we identified the corresponding avirulence effector,AvrRppC,which is secreted by P.polysora and triggers RppC-mediated resistance.Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance,indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production.Currently,RppC is the most frequently deployed SCR resistance gene in China,and a better understanding of its mode of action is crit-ical for extending its durability. | Ce Deng April Leonard James Cahill Meng Lv Yurong Li Shawn Thatcher Xueying Li Xiaodi Zhao Wenjie Du Zheng Li Huimin Li Victor Llaca Kevin Fengler Lisa Marshall Charlotte Harris Girma Tabor Zhimin Li Zhiqiang Tian Qinghua Yang Yanhui Chen Jihua Tang Xintao Wang Junjie Hao Jianbing Yan Zhibing Lai Xiaohong Fei Weibin Song Jinsheng Lai Xuecai Zhang Guoping Shu Yibo Wang Yuxiao Chang Weiling Zhu Wei Xiong Juan Sun Bailin Li Junqiang Ding | 2022 | Molecular Plant2022，15，5： | 6 |
| 4 | Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach显示文摘The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey’s Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach. | SUN JianDong XU Zhao HAO BaiLin | 2010 | Chinese Science Bulletin2010，55，22： | 5 |
| 5 | Shigella Strains Are Not Clones of Escherichia coli but Sister Species in the Genus Escherichia显示文摘Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Escherichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship. | Guanghong Zuo Zhao Xu Bailin Hao | 2013 | Genomics, Proteomics & Bioinformatics2013，11，1： | 5 |
| 6 | VERTICAL HEREDITY VS. HORIZONTAL GENE TRANSFER: A CHALLENGE TO BACTERIAL CLASSIFICATION显示文摘The diversity and classification of microbes has been a long-standing issue.Molecular phylogeny of the prokaryotes based on comparison of the 16S rRNA sequences of the small ribosomal subunit has led to a reasonable tree of life in the late 1970s. How-ever, the availability of more and more complete bacterial genomes has brought about complications instead of refinement of the tree. In particular, it turns out that different choice of genes may tell different history. This might be caused by possible horizontal gene transfer (HGT) among species. There is an urgent need to develop phylogenetic methods that make use of whole genome data. We describe a new approach in molecular phylogeny,namely, tree construction based on K-tuple frequency analysis of the genomic sequences.Putting aside the technicalities, we emphasize the transition from randomness to determin-ism when the string length K increases and try to comment on the challenge mentioned in the title. | HAO Bailin(Institute of Theoretical Physics, Academy of Chinese Sciences, Beijing 100080, China Senior International Fellow of the Santa Fe Institute T-Life Research Center, Fudan University,Shanghai 200433, China)QI Ji(Institute of Theoretical Physics, Beijing 100080, China) | 2003 | Journal of Systems Science & Complexity2003，16，3： | 3 |
| 7 | LVTree Viewer:An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics显示文摘We describe an interactive viewer for the All-Species Living Tree(LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner.In view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla(Proteobacteria and Firmicutes) to monophyletic clusters. | Guanghong Zuo Xiaoyang Zhi Zhao Xu Bailin Hao | 2016 | Genomics, Proteomics & Bioinformatics2016，14，2： | 3 |
| 8 | CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy显示文摘A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive,collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains.CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16 S r RNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://gffzz4ead16cf1e3949f6h9cxnqf6bcvqu660x.ffgz.tsg.suse.edu.cn/cvtree3/ without login requirements. | Guanghong Zuo Bailin Hao | 2015 | Genomics, Proteomics & Bioinformatics2015，13，5： | 3 |
| 9 | CVTree:A Phylogenetic-Tree Reconstruction Tool Based on Whole Genomes显示文摘 | Qi Ji Luo Hong Hao Bailin | 2004 | Nucleic Acids Research2004，32，2： | 1 |
| 10 | Whole Proteome Prokaryote Phylogeny Without Sequence Alignment:A K-String Composition Approach显示文摘 | Qi Ji Wang Bin Hao Bailin | 2004 | Journal Molecular Evolution2004，58，1： | 1 |
| 11 | Number of Periodic Orbits in Continuous Maps of the Interval – Complete Solution of the Counting Problem显示文摘 | Bailin Hao | 2000 | Annals of Combinatorics (-)2000，，3： | 1 |
| 12 | On monospecific genera in prokaryotic taxonomy显示文摘A monospecific genus contains a single species ever since it was proposed.Though formally more than half of the known prokaryotic genera are monospecific,we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides.Taking monophyly as a guiding principle,our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes,as provided by the LVTree Viewer and CVTree Web Server,respectively.The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis.Therefore,we refrain from making formal emendations for the time being. | Guanghong Zuo Bailin Hao | 2017 | Synthetic and Systems Biotechnology2017，2，3： | 0 |
| 13 | Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree显示文摘We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genomebased phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on wholegenome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy. | Guanghong Zuo Ji Qi Bailin Hao | 2018 | Genomics, Proteomics & Bioinformatics2018，16，5： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员