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  • 1
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    The genome of the model beetle and pest Tribolium castaneum (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-03-26
    Description: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tribolium Genome Sequencing Consortium -- Richards, Stephen -- Gibbs, Richard A -- Weinstock, George M -- Brown, Susan J -- Denell, Robin -- Beeman, Richard W -- Gibbs, Richard -- Bucher, Gregor -- Friedrich, Markus -- Grimmelikhuijzen, Cornelis J P -- Klingler, Martin -- Lorenzen, Marce -- Roth, Siegfried -- Schroder, Reinhard -- Tautz, Diethard -- Zdobnov, Evgeny M -- Muzny, Donna -- Attaway, Tony -- Bell, Stephanie -- Buhay, Christian J -- Chandrabose, Mimi N -- Chavez, Dean -- Clerk-Blankenburg, Kerstin P -- Cree, Andrew -- Dao, Marvin -- Davis, Clay -- Chacko, Joseph -- Dinh, Huyen -- Dugan-Rocha, Shannon -- Fowler, Gerald -- Garner, Toni T -- Garnes, Jeffrey -- Gnirke, Andreas -- Hawes, Alica -- Hernandez, Judith -- Hines, Sandra -- Holder, Michael -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Khan, Ziad Mohid -- Jackson, LaRonda -- Kovar, Christie -- Kowis, Andrea -- Lee, Sandra -- Lewis, Lora R -- Margolis, Jon -- Morgan, Margaret -- Nazareth, Lynne V -- Nguyen, Ngoc -- Okwuonu, Geoffrey -- Parker, David -- Ruiz, San-Juana -- Santibanez, Jireh -- Savard, Joel -- Scherer, Steven E -- Schneider, Brian -- Sodergren, Erica -- Vattahil, Selina -- Villasana, Donna -- White, Courtney S -- Wright, Rita -- Park, Yoonseong -- Lord, Jeff -- Oppert, Brenda -- Brown, Susan -- Wang, Liangjiang -- Weinstock, George -- Liu, Yue -- Worley, Kim -- Elsik, Christine G -- Reese, Justin T -- Elhaik, Eran -- Landan, Giddy -- Graur, Dan -- Arensburger, Peter -- Atkinson, Peter -- Beidler, Jim -- Demuth, Jeffery P -- Drury, Douglas W -- Du, Yu-Zhou -- Fujiwara, Haruhiko -- Maselli, Vincenza -- Osanai, Mizuko -- Robertson, Hugh M -- Tu, Zhijian -- Wang, Jian-jun -- Wang, Suzhi -- Song, Henry -- Zhang, Lan -- Werner, Doreen -- Stanke, Mario -- Morgenstern, Burkhard -- Solovyev, Victor -- Kosarev, Peter -- Brown, Garth -- Chen, Hsiu-Chuan -- Ermolaeva, Olga -- Hlavina, Wratko -- Kapustin, Yuri -- Kiryutin, Boris -- Kitts, Paul -- Maglott, Donna -- Pruitt, Kim -- Sapojnikov, Victor -- Souvorov, Alexandre -- Mackey, Aaron J -- Waterhouse, Robert M -- Wyder, Stefan -- Kriventseva, Evgenia V -- Kadowaki, Tatsuhiko -- Bork, Peer -- Aranda, Manuel -- Bao, Riyue -- Beermann, Anke -- Berns, Nicola -- Bolognesi, Renata -- Bonneton, Francois -- Bopp, Daniel -- Butts, Thomas -- Chaumot, Arnaud -- Denell, Robin E -- Ferrier, David E K -- Gordon, Cassondra M -- Jindra, Marek -- Lan, Que -- Lattorff, H Michael G -- Laudet, Vincent -- von Levetsow, Cornelia -- Liu, Zhenyi -- Lutz, Rebekka -- Lynch, Jeremy A -- da Fonseca, Rodrigo Nunes -- Posnien, Nico -- Reuter, Rolf -- Schinko, Johannes B -- Schmitt, Christian -- Schoppmeier, Michael -- Shippy, Teresa D -- Simonnet, Franck -- Marques-Souza, Henrique -- Tomoyasu, Yoshinori -- Trauner, Jochen -- Van der Zee, Maurijn -- Vervoort, Michel -- Wittkopp, Nadine -- Wimmer, Ernst A -- Yang, Xiaoyun -- Jones, Andrew K -- Sattelle, David B -- Ebert, Paul R -- Nelson, David -- Scott, Jeffrey G -- Muthukrishnan, Subbaratnam -- Kramer, Karl J -- Arakane, Yasuyuki -- Zhu, Qingsong -- Hogenkamp, David -- Dixit, Radhika -- Jiang, Haobo -- Zou, Zhen -- Marshall, Jeremy -- Elpidina, Elena -- Vinokurov, Konstantin -- Oppert, Cris -- Evans, Jay -- Lu, Zhiqiang -- Zhao, Picheng -- Sumathipala, Niranji -- Altincicek, Boran -- Vilcinskas, Andreas -- Williams, Michael -- Hultmark, Dan -- Hetru, Charles -- Hauser, Frank -- Cazzamali, Giuseppe -- Williamson, Michael -- Li, Bin -- Tanaka, Yoshiaki -- Predel, Reinhard -- Neupert, Susanne -- Schachtner, Joachim -- Verleyen, Peter -- Raible, Florian -- Walden, Kimberly K O -- Angeli, Sergio -- Foret, Sylvain -- Schuetz, Stefan -- Maleszka, Ryszard -- Miller, Sherry C -- Grossmann, Daniela -- BBS/B/12067/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/12067/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- R01 GM058634/GM/NIGMS NIH HHS/ -- R01 HD029594/HD/NICHD NIH HHS/ -- R01 HD029594-16/HD/NICHD NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):949-55. doi: 10.1038/nature06784. Epub 2008 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA. stephenr@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18362917" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Body Patterning/genetics ; Cytochrome P-450 Enzyme System/genetics ; DNA Transposable Elements/genetics ; Genes, Insect/*genetics ; Genome, Insect/*genetics ; Growth and Development/genetics ; Humans ; Insecticides/pharmacology ; Neurotransmitter Agents/genetics ; Oogenesis/genetics ; Phylogeny ; Proteome/genetics ; RNA Interference ; Receptors, G-Protein-Coupled/genetics ; Receptors, Odorant/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Taste/genetics ; Telomere/genetics ; Tribolium/classification/embryology/*genetics/physiology ; Vision, Ocular/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-02
    Description: The early evolution of the major groups of derived non-avialan theropods is still not well understood, mainly because of their poor fossil record in the Jurassic. A well-known result of this problem is the 'temporal paradox' argument that is sometimes made against the theropod hypothesis of avian origins. Here we report on an exceptionally well-preserved small theropod specimen collected from the earliest Late Jurassic Tiaojishan Formation of western Liaoning, China. The specimen is referable to the Troodontidae, which are among the theropods most closely related to birds. This new find refutes the 'temporal paradox'1 and provides significant information on the temporal framework of theropod divergence. Furthermore, the extensive feathering of this specimen, particularly the attachment of long pennaceous feathers to the pes, sheds new light on the early evolution of feathers and demonstrates the complex distribution of skeletal and integumentary features close to the dinosaur-bird transition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Dongyu -- Hou, Lianhai -- Zhang, Lijun -- Xu, Xing -- England -- Nature. 2009 Oct 1;461(7264):640-3. doi: 10.1038/nature08322.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Paleontological Institute, Shenyang Normal University, 253 North Huanghe Street, Shenyang 110034, China. hudongyu@synu.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794491" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Birds/anatomy & histology/classification ; Calibration ; China ; Dinosaurs/*anatomy & histology/*classification ; Feathers/*anatomy & histology ; Flight, Animal ; Foot/anatomy & histology ; *Fossils ; Metatarsus/*anatomy & histology ; Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Lower Cambrian vendobionts from China and early diploblast evolution (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-06
    Description: Ediacaran assemblages immediately predate the Cambrian explosion of metazoans and should have played a crucial role in this radiation. Their wider relationships, however, have remained refractory and difficult to integrate with early metazoan phylogeny. Here, we describe a frondlike fossil, Stromatoveris (S. psygmoglena sp. nov.), from the Lower Cambrian Chengjiang Lagerstatte (Yunnan, China) that is strikingly similar to Ediacaran vendobionts. The exquisite preservation reveals closely spaced branches, probably ciliated, that appear to represent precursors of the diagnostic comb rows of ctenophores. Therefore, this finding has important implications for the early evolution of this phylum and related diploblasts, some of which independently evolved a frondose habit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shu, D-G -- Morris, S Conway -- Han, J -- Li, Y -- Zhang, X-L -- Hua, H -- Zhang, Z-F -- Liu, J-N -- Guo, J-F -- Yao, Y -- Yasui, K -- New York, N.Y. -- Science. 2006 May 5;312(5774):731-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Early Life Institute and Key Laboratory of Continental Dynamics, Northwest University, Xi'an 710069, China. elidgshu@nwu.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16675697" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; China ; *Fossils ; Geologic Sediments ; Invertebrates/*anatomy & histology/*classification ; Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    A new species of yunnanozoan with implications for deuterostome evolution (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-01
    Description: Yunnanozoans are a distinctive clade of Lower Cambrian metazoans. Although widely accepted as deuterostomes, their exact placement within this superphylum is controversial. Here we describe a new species of Haikouella (H. jianshanensis) from the Chengjiang Lagerstatte (Yunnan, China) with exceptional preservation of a number of features. These include external gills, which suggest that the origin of the pharyngeal clefts was independent of the gills. The diagnostic branchial arches of chordates may, therefore, be composite structures. No evidence was found for the chordate-like structures that have been described in other yunnanozoans. We propose that yunnanozoans are stem-group deuterostomes, allied to the vetulicolians.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shu, Degan -- Morris, Simon Conway -- Zhang, Z F -- Liu, J N -- Han, Jian -- Chen, Ling -- Zhang, X L -- Yasui, K -- Li, Yong -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1380-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Early Life Institute and Department of Geology, Northwest University, Xi'an 710069, China. elidgshu@nwu.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610301" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; China ; Chordata, Nonvertebrate/*anatomy & histology/*classification ; Digestive System/anatomy & histology ; *Fossils ; Gills/anatomy & histology ; Mouth/anatomy & histology ; Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Highly pathogenic H5N1 influenza virus infection in migratory birds (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-07-08
    Description: H5N1 avian influenza virus (AIV) has emerged as a pathogenic entity for a variety of species, including humans, in recent years. Here we report an outbreak among migratory birds on Lake Qinghaihu, China, in May and June 2005, in which more than a thousand birds were affected. Pancreatic necrosis and abnormal neurological symptoms were the major clinical features. Sequencing of the complete genomes of four H5N1 AIV strains revealed them to be reassortants related to a peregrine falcon isolate from Hong Kong and to have known highly pathogenic characteristics. Experimental animal infections reproduced typical highly pathogenic AIV infection symptoms and pathology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, J -- Xiao, H -- Lei, F -- Zhu, Q -- Qin, K -- Zhang, X-W -- Zhang, X-L -- Zhao, D -- Wang, G -- Feng, Y -- Ma, J -- Liu, W -- Wang, J -- Gao, G F -- New York, N.Y. -- Science. 2005 Aug 19;309(5738):1206. Epub 2005 Jul 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Veterinary Medicine, China Agricultural University, Beijing 100094, China. jhl@cau.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16000410" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animal Migration ; Animals ; Birds/virology ; Charadriiformes/*virology ; Chickens ; China/epidemiology ; Disease Outbreaks/*veterinary ; Geese/*virology ; Genome, Viral ; *Influenza A Virus, H5N1 Subtype ; Influenza A virus/classification/genetics/isolation & purification/*pathogenicity ; Influenza in Birds/*epidemiology/pathology/*virology ; Mice ; Molecular Sequence Data ; Phylogeny ; Reassortant Viruses/genetics/pathogenicity ; Virulence
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-12-22
    Description: Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paterson, Andrew H -- Wendel, Jonathan F -- Gundlach, Heidrun -- Guo, Hui -- Jenkins, Jerry -- Jin, Dianchuan -- Llewellyn, Danny -- Showmaker, Kurtis C -- Shu, Shengqiang -- Udall, Joshua -- Yoo, Mi-jeong -- Byers, Robert -- Chen, Wei -- Doron-Faigenboim, Adi -- Duke, Mary V -- Gong, Lei -- Grimwood, Jane -- Grover, Corrinne -- Grupp, Kara -- Hu, Guanjing -- Lee, Tae-ho -- Li, Jingping -- Lin, Lifeng -- Liu, Tao -- Marler, Barry S -- Page, Justin T -- Roberts, Alison W -- Romanel, Elisson -- Sanders, William S -- Szadkowski, Emmanuel -- Tan, Xu -- Tang, Haibao -- Xu, Chunming -- Wang, Jinpeng -- Wang, Zining -- Zhang, Dong -- Zhang, Lan -- Ashrafi, Hamid -- Bedon, Frank -- Bowers, John E -- Brubaker, Curt L -- Chee, Peng W -- Das, Sayan -- Gingle, Alan R -- Haigler, Candace H -- Harker, David -- Hoffmann, Lucia V -- Hovav, Ran -- Jones, Donald C -- Lemke, Cornelia -- Mansoor, Shahid -- ur Rahman, Mehboob -- Rainville, Lisa N -- Rambani, Aditi -- Reddy, Umesh K -- Rong, Jun-kang -- Saranga, Yehoshua -- Scheffler, Brian E -- Scheffler, Jodi A -- Stelly, David M -- Triplett, Barbara A -- Van Deynze, Allen -- Vaslin, Maite F S -- Waghmare, Vijay N -- Walford, Sally A -- Wright, Robert J -- Zaki, Essam A -- Zhang, Tianzhen -- Dennis, Elizabeth S -- Mayer, Klaus F X -- Peterson, Daniel G -- Rokhsar, Daniel S -- Wang, Xiyin -- Schmutz, Jeremy -- England -- Nature. 2012 Dec 20;492(7429):423-7. doi: 10.1038/nature11798.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23257886" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; *Biological Evolution ; Cacao/genetics ; Chromosomes, Plant/genetics ; *Cotton Fiber ; Diploidy ; Gene Duplication/genetics ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Gossypium/classification/*genetics ; Molecular Sequence Annotation ; Phylogeny ; *Polyploidy ; Vitis/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    A map of rice genome variation reveals the origin of cultivated rice (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-10-05
    Description: Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Xuehui -- Kurata, Nori -- Wei, Xinghua -- Wang, Zi-Xuan -- Wang, Ahong -- Zhao, Qiang -- Zhao, Yan -- Liu, Kunyan -- Lu, Hengyun -- Li, Wenjun -- Guo, Yunli -- Lu, Yiqi -- Zhou, Congcong -- Fan, Danlin -- Weng, Qijun -- Zhu, Chuanrang -- Huang, Tao -- Zhang, Lei -- Wang, Yongchun -- Feng, Lei -- Furuumi, Hiroyasu -- Kubo, Takahiko -- Miyabayashi, Toshie -- Yuan, Xiaoping -- Xu, Qun -- Dong, Guojun -- Zhan, Qilin -- Li, Canyang -- Fujiyama, Asao -- Toyoda, Atsushi -- Lu, Tingting -- Feng, Qi -- Qian, Qian -- Li, Jiayang -- Han, Bin -- England -- Nature. 2012 Oct 25;490(7421):497-501. doi: 10.1038/nature11532. Epub 2012 Oct 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23034647" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; Breeding/history ; Crops, Agricultural/classification/*genetics/growth & development ; *Evolution, Molecular ; Genetic Variation/*genetics ; Genome, Plant/*genetics ; Genomics ; *Geographic Mapping ; History, Ancient ; Oryza/classification/*genetics/growth & development ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    A catalog of reference genomes from the human microbiome (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-05-22
    Description: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940224/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Human Microbiome Jumpstart Reference Strains Consortium -- Nelson, Karen E -- Weinstock, George M -- Highlander, Sarah K -- Worley, Kim C -- Creasy, Heather Huot -- Wortman, Jennifer Russo -- Rusch, Douglas B -- Mitreva, Makedonka -- Sodergren, Erica -- Chinwalla, Asif T -- Feldgarden, Michael -- Gevers, Dirk -- Haas, Brian J -- Madupu, Ramana -- Ward, Doyle V -- Birren, Bruce W -- Gibbs, Richard A -- Methe, Barbara -- Petrosino, Joseph F -- Strausberg, Robert L -- Sutton, Granger G -- White, Owen R -- Wilson, Richard K -- Durkin, Scott -- Giglio, Michelle Gwinn -- Gujja, Sharvari -- Howarth, Clint -- Kodira, Chinnappa D -- Kyrpides, Nikos -- Mehta, Teena -- Muzny, Donna M -- Pearson, Matthew -- Pepin, Kymberlie -- Pati, Amrita -- Qin, Xiang -- Yandava, Chandri -- Zeng, Qiandong -- Zhang, Lan -- Berlin, Aaron M -- Chen, Lei -- Hepburn, Theresa A -- Johnson, Justin -- McCorrison, Jamison -- Miller, Jason -- Minx, Pat -- Nusbaum, Chad -- Russ, Carsten -- Sykes, Sean M -- Tomlinson, Chad M -- Young, Sarah -- Warren, Wesley C -- Badger, Jonathan -- Crabtree, Jonathan -- Markowitz, Victor M -- Orvis, Joshua -- Cree, Andrew -- Ferriera, Steve -- Fulton, Lucinda L -- Fulton, Robert S -- Gillis, Marcus -- Hemphill, Lisa D -- Joshi, Vandita -- Kovar, Christie -- Torralba, Manolito -- Wetterstrand, Kris A -- Abouellleil, Amr -- Wollam, Aye M -- Buhay, Christian J -- Ding, Yan -- Dugan, Shannon -- FitzGerald, Michael G -- Holder, Mike -- Hostetler, Jessica -- Clifton, Sandra W -- Allen-Vercoe, Emma -- Earl, Ashlee M -- Farmer, Candace N -- Liolios, Konstantinos -- Surette, Michael G -- Xu, Qiang -- Pohl, Craig -- Wilczek-Boney, Katarzyna -- Zhu, Dianhui -- HHSN272200900017C/PHS HHS/ -- N01 AI30071/AI/NIAID NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-04/HG/NHGRI NIH HHS/ -- U54 HG003273-04S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05/HG/NHGRI NIH HHS/ -- U54 HG003273-05S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05S2/HG/NHGRI NIH HHS/ -- U54 HG003273-06/HG/NHGRI NIH HHS/ -- U54 HG003273-06S1/HG/NHGRI NIH HHS/ -- U54 HG003273-06S2/HG/NHGRI NIH HHS/ -- U54 HG003273-07/HG/NHGRI NIH HHS/ -- U54 HG003273-08/HG/NHGRI NIH HHS/ -- U54 HG004973/HG/NHGRI NIH HHS/ -- U54 HG004973-01/HG/NHGRI NIH HHS/ -- U54 HG004973-02/HG/NHGRI NIH HHS/ -- U54-AI084844/AI/NIAID NIH HHS/ -- U54-HG003079/HG/NHGRI NIH HHS/ -- U54-HG003273/HG/NHGRI NIH HHS/ -- U54-HG004968/HG/NHGRI NIH HHS/ -- U54-HG004969/HG/NHGRI NIH HHS/ -- U54-HG004973/HG/NHGRI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 May 21;328(5981):994-9. doi: 10.1126/science.1183605.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489017" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/classification/genetics ; Bacterial Proteins/chemistry/genetics ; Biodiversity ; Computational Biology ; Databases, Genetic ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Genetic Variation ; Genome, Archaeal ; *Genome, Bacterial ; Humans ; Metagenome/*genetics ; Metagenomics/methods/standards ; Mouth/microbiology ; Peptides/chemistry/genetics ; Phylogeny ; Respiratory System/microbiology ; *Sequence Analysis, DNA/standards ; Skin/microbiology ; Urogenital System/microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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