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  • 1
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    Growth in emission transfers via international trade from 1990 to 2008 [Sustainability Science] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-05-25
    Description: Despite the emergence of regional climate policies, growth in global CO2 emissions has remained strong. From 1990 to 2008 CO2 emissions in developed countries (defined as countries with emission-reduction commitments in the Kyoto Protocol, Annex B) have stabilized, but emissions in developing countries (non-Annex B) have doubled. Some studies suggest that the stabilization of emissions in developed countries was partially because of growing imports from developing countries. To quantify the growth in emission transfers via international trade, we developed a trade-linked global database for CO2 emissions covering 113 countries and 57 economic sectors from 1990 to 2008. We find that the emissions from the production of traded goods and services have increased from 4.3 Gt CO2 in 1990 (20% of global emissions) to 7.8 Gt CO2 in 2008 (26%). Most developed countries have increased their consumption-based emissions faster than their territorial emissions, and non–energy-intensive manufacturing had a key role in the emission transfers. The net emission transfers via international trade from developing to developed countries increased from 0.4 Gt CO2 in 1990 to 1.6 Gt CO2 in 2008, which exceeds the Kyoto Protocol emission reductions. Our results indicate that international trade is a significant factor in explaining the change in emissions in many countries, from both a production and consumption perspective. We suggest that countries monitor emission transfers via international trade, in addition to territorial emissions, to ensure progress toward stabilization of global greenhouse gas emissions.
    Keywords: Sustainability Science
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Genome analysis of the platypus reveals unique signatures of evolution (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-05-10
    Description: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040/" 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/PMC2803040/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Wesley C -- Hillier, LaDeana W -- Marshall Graves, Jennifer A -- Birney, Ewan -- Ponting, Chris P -- Grutzner, Frank -- Belov, Katherine -- Miller, Webb -- Clarke, Laura -- Chinwalla, Asif T -- Yang, Shiaw-Pyng -- Heger, Andreas -- Locke, Devin P -- Miethke, Pat -- Waters, Paul D -- Veyrunes, Frederic -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Wallis, John -- Puente, Xose S -- Lopez-Otin, Carlos -- Ordonez, Gonzalo R -- Eichler, Evan E -- Chen, Lin -- Cheng, Ze -- Deakin, Janine E -- Alsop, Amber -- Thompson, Katherine -- Kirby, Patrick -- Papenfuss, Anthony T -- Wakefield, Matthew J -- Olender, Tsviya -- Lancet, Doron -- Huttley, Gavin A -- Smit, Arian F A -- Pask, Andrew -- Temple-Smith, Peter -- Batzer, Mark A -- Walker, Jerilyn A -- Konkel, Miriam K -- Harris, Robert S -- Whittington, Camilla M -- Wong, Emily S W -- Gemmell, Neil J -- Buschiazzo, Emmanuel -- Vargas Jentzsch, Iris M -- Merkel, Angelika -- Schmitz, Juergen -- Zemann, Anja -- Churakov, Gennady -- Kriegs, Jan Ole -- Brosius, Juergen -- Murchison, Elizabeth P -- Sachidanandam, Ravi -- Smith, Carly -- Hannon, Gregory J -- Tsend-Ayush, Enkhjargal -- McMillan, Daniel -- Attenborough, Rosalind -- Rens, Willem -- Ferguson-Smith, Malcolm -- Lefevre, Christophe M -- Sharp, Julie A -- Nicholas, Kevin R -- Ray, David A -- Kube, Michael -- Reinhardt, Richard -- Pringle, Thomas H -- Taylor, James -- Jones, Russell C -- Nixon, Brett -- Dacheux, Jean-Louis -- Niwa, Hitoshi -- Sekita, Yoko -- Huang, Xiaoqiu -- Stark, Alexander -- Kheradpour, Pouya -- Kellis, Manolis -- Flicek, Paul -- Chen, Yuan -- Webber, Caleb -- Hardison, Ross -- Nelson, Joanne -- Hallsworth-Pepin, Kym -- Delehaunty, Kim -- Markovic, Chris -- Minx, Pat -- Feng, Yucheng -- Kremitzki, Colin -- Mitreva, Makedonka -- Glasscock, Jarret -- Wylie, Todd -- Wohldmann, Patricia -- Thiru, Prathapan -- Nhan, Michael N -- Pohl, Craig S -- Smith, Scott M -- Hou, Shunfeng -- Nefedov, Mikhail -- de Jong, Pieter J -- Renfree, Marilyn B -- Mardis, Elaine R -- Wilson, Richard K -- 062023/Wellcome Trust/United Kingdom -- HG002238/HG/NHGRI NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA013106-37/CA/NCI NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-02/HG/NHGRI NIH HHS/ -- R01HG02385/HG/NHGRI NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. wwarren@wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18464734" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Dentition ; *Evolution, Molecular ; Female ; Genome/*genetics ; Genomic Imprinting/genetics ; Humans ; Immunity/genetics ; Male ; Mammals/genetics ; MicroRNAs/genetics ; Milk Proteins/genetics ; Phylogeny ; Platypus/*genetics/immunology/physiology ; Receptors, Odorant/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Reptiles/genetics ; Sequence Analysis, DNA ; Spermatozoa/metabolism ; Venoms/genetics ; Zona Pellucida/metabolism
    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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    DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-11-07
    Description: Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the past two decades, because most of the genetic events that initiate the disease remain undiscovered. Whole-genome sequencing is now possible at a reasonable cost and timeframe to use this approach for the unbiased discovery of tumour-specific somatic mutations that alter the protein-coding genes. Here we present the results obtained from sequencing a typical acute myeloid leukaemia genome, and its matched normal counterpart obtained from the same patient's skin. We discovered ten genes with acquired mutations; two were previously described mutations that are thought to contribute to tumour progression, and eight were new mutations present in virtually all tumour cells at presentation and relapse, the function of which is not yet known. Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603574/" 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/PMC2603574/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ley, Timothy J -- Mardis, Elaine R -- Ding, Li -- Fulton, Bob -- McLellan, Michael D -- Chen, Ken -- Dooling, David -- Dunford-Shore, Brian H -- McGrath, Sean -- Hickenbotham, Matthew -- Cook, Lisa -- Abbott, Rachel -- Larson, David E -- Koboldt, Dan C -- Pohl, Craig -- Smith, Scott -- Hawkins, Amy -- Abbott, Scott -- Locke, Devin -- Hillier, Ladeana W -- Miner, Tracie -- Fulton, Lucinda -- Magrini, Vincent -- Wylie, Todd -- Glasscock, Jarret -- Conyers, Joshua -- Sander, Nathan -- Shi, Xiaoqi -- Osborne, John R -- Minx, Patrick -- Gordon, David -- Chinwalla, Asif -- Zhao, Yu -- Ries, Rhonda E -- Payton, Jacqueline E -- Westervelt, Peter -- Tomasson, Michael H -- Watson, Mark -- Baty, Jack -- Ivanovich, Jennifer -- Heath, Sharon -- Shannon, William D -- Nagarajan, Rakesh -- Walter, Matthew J -- Link, Daniel C -- Graubert, Timothy A -- DiPersio, John F -- Wilson, Richard K -- U54 HG002042/HG/NHGRI NIH HHS/ -- U54 HG002042-05/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Nov 6;456(7218):66-72. doi: 10.1038/nature07485.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987736" target="_blank"〉PubMed〈/a〉
    Keywords: Case-Control Studies ; Disease Progression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/*genetics ; Genome, Human/*genetics ; Genomics ; Humans ; Leukemia, Myeloid, Acute/*genetics ; Mutagenesis, Insertional ; Mutation ; Polymorphism, Single Nucleotide ; Recurrence ; Sequence Analysis, DNA ; Sequence Deletion ; Skin/metabolism
    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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  • 4
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    Evolutionary and biomedical insights from the rhesus macaque genome (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhesus Macaque Genome Sequencing and Analysis Consortium -- Gibbs, Richard A -- Rogers, Jeffrey -- Katze, Michael G -- Bumgarner, Roger -- Weinstock, George M -- Mardis, Elaine R -- Remington, Karin A -- Strausberg, Robert L -- Venter, J Craig -- Wilson, Richard K -- Batzer, Mark A -- Bustamante, Carlos D -- Eichler, Evan E -- Hahn, Matthew W -- Hardison, Ross C -- Makova, Kateryna D -- Miller, Webb -- Milosavljevic, Aleksandar -- Palermo, Robert E -- Siepel, Adam -- Sikela, James M -- Attaway, Tony -- Bell, Stephanie -- Bernard, Kelly E -- Buhay, Christian J -- Chandrabose, Mimi N -- Dao, Marvin -- Davis, Clay -- Delehaunty, Kimberly D -- Ding, Yan -- Dinh, Huyen H -- Dugan-Rocha, Shannon -- Fulton, Lucinda A -- Gabisi, Ramatu Ayiesha -- Garner, Toni T -- Godfrey, Jennifer -- Hawes, Alicia C -- Hernandez, Judith -- Hines, Sandra -- Holder, Michael -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Khan, Ziad Mohid -- Kirkness, Ewen F -- Cree, Andrew -- Fowler, R Gerald -- Lee, Sandra -- Lewis, Lora R -- Li, Zhangwan -- Liu, Yih-Shin -- Moore, Stephanie M -- Muzny, Donna -- Nazareth, Lynne V -- Ngo, Dinh Ngoc -- Okwuonu, Geoffrey O -- Pai, Grace -- Parker, David -- Paul, Heidie A -- Pfannkoch, Cynthia -- Pohl, Craig S -- Rogers, Yu-Hui -- Ruiz, San Juana -- Sabo, Aniko -- Santibanez, Jireh -- Schneider, Brian W -- Smith, Scott M -- Sodergren, Erica -- Svatek, Amanda F -- Utterback, Teresa R -- Vattathil, Selina -- Warren, Wesley -- White, Courtney Sherell -- Chinwalla, Asif T -- Feng, Yucheng -- Halpern, Aaron L -- Hillier, Ladeana W -- Huang, Xiaoqiu -- Minx, Pat -- Nelson, Joanne O -- Pepin, Kymberlie H -- Qin, Xiang -- Sutton, Granger G -- Venter, Eli -- Walenz, Brian P -- Wallis, John W -- Worley, Kim C -- Yang, Shiaw-Pyng -- Jones, Steven M -- Marra, Marco A -- Rocchi, Mariano -- Schein, Jacqueline E -- Baertsch, Robert -- Clarke, Laura -- Csuros, Miklos -- Glasscock, Jarret -- Harris, R Alan -- Havlak, Paul -- Jackson, Andrew R -- Jiang, Huaiyang -- Liu, Yue -- Messina, David N -- Shen, Yufeng -- Song, Henry Xing-Zhi -- Wylie, Todd -- Zhang, Lan -- Birney, Ewan -- Han, Kyudong -- Konkel, Miriam K -- Lee, Jungnam -- Smit, Arian F A -- Ullmer, Brygg -- Wang, Hui -- Xing, Jinchuan -- Burhans, Richard -- Cheng, Ze -- Karro, John E -- Ma, Jian -- Raney, Brian -- She, Xinwei -- Cox, Michael J -- Demuth, Jeffery P -- Dumas, Laura J -- Han, Sang-Gook -- Hopkins, Janet -- Karimpour-Fard, Anis -- Kim, Young H -- Pollack, Jonathan R -- Vinar, Tomas -- Addo-Quaye, Charles -- Degenhardt, Jeremiah -- Denby, Alexandra -- Hubisz, Melissa J -- Indap, Amit -- Kosiol, Carolin -- Lahn, Bruce T -- Lawson, Heather A -- Marklein, Alison -- Nielsen, Rasmus -- Vallender, Eric J -- Clark, Andrew G -- Ferguson, Betsy -- Hernandez, Ryan D -- Hirani, Kashif -- Kehrer-Sawatzki, Hildegard -- Kolb, Jessica -- Patil, Shobha -- Pu, Ling-Ling -- Ren, Yanru -- Smith, David Glenn -- Wheeler, David A -- Schenck, Ian -- Ball, Edward V -- Chen, Rui -- Cooper, David N -- Giardine, Belinda -- Hsu, Fan -- Kent, W James -- Lesk, Arthur -- Nelson, David L -- O'brien, William E -- Prufer, Kay -- Stenson, Peter D -- Wallace, James C -- Ke, Hui -- Liu, Xiao-Ming -- Wang, Peng -- Xiang, Andy Peng -- Yang, Fan -- Barber, Galt P -- Haussler, David -- Karolchik, Donna -- Kern, Andy D -- Kuhn, Robert M -- Smith, Kayla E -- Zwieg, Ann S -- 062023/Wellcome Trust/United Kingdom -- R01 HG002939/HG/NHGRI NIH HHS/ -- U54 HG003068/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):222-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. agibbs@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431167" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomedical Research ; *Evolution, Molecular ; Female ; Gene Duplication ; Gene Rearrangement ; Genetic Diseases, Inborn ; Genetic Variation ; *Genome ; Humans ; Macaca mulatta/*genetics ; Male ; Multigene Family ; Mutation ; Pan troglodytes/genetics ; Sequence Analysis, DNA ; Species Specificity
    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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  • 5
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    The B73 maize genome: complexity, diversity, and dynamics (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schnable, Patrick S -- Ware, Doreen -- Fulton, Robert S -- Stein, Joshua C -- Wei, Fusheng -- Pasternak, Shiran -- Liang, Chengzhi -- Zhang, Jianwei -- Fulton, Lucinda -- Graves, Tina A -- Minx, Patrick -- Reily, Amy Denise -- Courtney, Laura -- Kruchowski, Scott S -- Tomlinson, Chad -- Strong, Cindy -- Delehaunty, Kim -- Fronick, Catrina -- Courtney, Bill -- Rock, Susan M -- Belter, Eddie -- Du, Feiyu -- Kim, Kyung -- Abbott, Rachel M -- Cotton, Marc -- Levy, Andy -- Marchetto, Pamela -- Ochoa, Kerri -- Jackson, Stephanie M -- Gillam, Barbara -- Chen, Weizu -- Yan, Le -- Higginbotham, Jamey -- Cardenas, Marco -- Waligorski, Jason -- Applebaum, Elizabeth -- Phelps, Lindsey -- Falcone, Jason -- Kanchi, Krishna -- Thane, Thynn -- Scimone, Adam -- Thane, Nay -- Henke, Jessica -- Wang, Tom -- Ruppert, Jessica -- Shah, Neha -- Rotter, Kelsi -- Hodges, Jennifer -- Ingenthron, Elizabeth -- Cordes, Matt -- Kohlberg, Sara -- Sgro, Jennifer -- Delgado, Brandon -- Mead, Kelly -- Chinwalla, Asif -- Leonard, Shawn -- Crouse, Kevin -- Collura, Kristi -- Kudrna, Dave -- Currie, Jennifer -- He, Ruifeng -- Angelova, Angelina -- Rajasekar, Shanmugam -- Mueller, Teri -- Lomeli, Rene -- Scara, Gabriel -- Ko, Ara -- Delaney, Krista -- Wissotski, Marina -- Lopez, Georgina -- Campos, David -- Braidotti, Michele -- Ashley, Elizabeth -- Golser, Wolfgang -- Kim, HyeRan -- Lee, Seunghee -- Lin, Jinke -- Dujmic, Zeljko -- Kim, Woojin -- Talag, Jayson -- Zuccolo, Andrea -- Fan, Chuanzhu -- Sebastian, Aswathy -- Kramer, Melissa -- Spiegel, Lori -- Nascimento, Lidia -- Zutavern, Theresa -- Miller, Beth -- Ambroise, Claude -- Muller, Stephanie -- Spooner, Will -- Narechania, Apurva -- Ren, Liya -- Wei, Sharon -- Kumari, Sunita -- Faga, Ben -- Levy, Michael J -- McMahan, Linda -- Van Buren, Peter -- Vaughn, Matthew W -- Ying, Kai -- Yeh, Cheng-Ting -- Emrich, Scott J -- Jia, Yi -- Kalyanaraman, Ananth -- Hsia, An-Ping -- Barbazuk, W Brad -- Baucom, Regina S -- Brutnell, Thomas P -- Carpita, Nicholas C -- Chaparro, Cristian -- Chia, Jer-Ming -- Deragon, Jean-Marc -- Estill, James C -- Fu, Yan -- Jeddeloh, Jeffrey A -- Han, Yujun -- Lee, Hyeran -- Li, Pinghua -- Lisch, Damon R -- Liu, Sanzhen -- Liu, Zhijie -- Nagel, Dawn Holligan -- McCann, Maureen C -- SanMiguel, Phillip -- Myers, Alan M -- Nettleton, Dan -- Nguyen, John -- Penning, Bryan W -- Ponnala, Lalit -- Schneider, Kevin L -- Schwartz, David C -- Sharma, Anupma -- Soderlund, Carol -- Springer, Nathan M -- Sun, Qi -- Wang, Hao -- Waterman, Michael -- Westerman, Richard -- Wolfgruber, Thomas K -- Yang, Lixing -- Yu, Yeisoo -- Zhang, Lifang -- Zhou, Shiguo -- Zhu, Qihui -- Bennetzen, Jeffrey L -- Dawe, R Kelly -- Jiang, Jiming -- Jiang, Ning -- Presting, Gernot G -- Wessler, Susan R -- Aluru, Srinivas -- Martienssen, Robert A -- Clifton, Sandra W -- McCombie, W Richard -- Wing, Rod A -- Wilson, Richard K -- New York, N.Y. -- Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965430" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Centromere/genetics ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Crops, Agricultural/genetics ; DNA Copy Number Variations ; DNA Methylation ; DNA Transposable Elements ; DNA, Plant/genetics ; Genes, Plant ; *Genetic Variation ; *Genome, Plant ; Inbreeding ; MicroRNAs/genetics ; Molecular Sequence Data ; Ploidies ; RNA, Plant/genetics ; Recombination, Genetic ; Retroelements ; *Sequence Analysis, DNA ; Zea mays/*genetics
    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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    Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-15
    Description: Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971456/" 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/PMC3971456/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baxter, Laura -- Tripathy, Sucheta -- Ishaque, Naveed -- Boot, Nico -- Cabral, Adriana -- Kemen, Eric -- Thines, Marco -- Ah-Fong, Audrey -- Anderson, Ryan -- Badejoko, Wole -- Bittner-Eddy, Peter -- Boore, Jeffrey L -- Chibucos, Marcus C -- Coates, Mary -- Dehal, Paramvir -- Delehaunty, Kim -- Dong, Suomeng -- Downton, Polly -- Dumas, Bernard -- Fabro, Georgina -- Fronick, Catrina -- Fuerstenberg, Susan I -- Fulton, Lucinda -- Gaulin, Elodie -- Govers, Francine -- Hughes, Linda -- Humphray, Sean -- Jiang, Rays H Y -- Judelson, Howard -- Kamoun, Sophien -- Kyung, Kim -- Meijer, Harold -- Minx, Patrick -- Morris, Paul -- Nelson, Joanne -- Phuntumart, Vipa -- Qutob, Dinah -- Rehmany, Anne -- Rougon-Cardoso, Alejandra -- Ryden, Peter -- Torto-Alalibo, Trudy -- Studholme, David -- Wang, Yuanchao -- Win, Joe -- Wood, Jo -- Clifton, Sandra W -- Rogers, Jane -- Van den Ackerveken, Guido -- Jones, Jonathan D G -- McDowell, John M -- Beynon, Jim -- Tyler, Brett M -- 079643/Wellcome Trust/United Kingdom -- BB/C509123/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E007120/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E024815/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E024882/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F0161901/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G015244/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- EP/F500025/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- T12144/Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1549-51. doi: 10.1126/science.1195203.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148394" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Sequence ; Arabidopsis/*parasitology ; Enzymes/genetics ; *Evolution, Molecular ; Gene Dosage ; Genes ; *Genome ; Host-Pathogen Interactions ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Oomycetes/*genetics/*growth & development/pathogenicity/physiology ; Phytophthora/genetics ; Plant Diseases/*parasitology ; Polymorphism, Single Nucleotide ; Proteins/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Spores/physiology ; Synteny ; Virulence Factors/genetics
    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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  • 7
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    A high-resolution map of human evolutionary constraint using 29 mammals (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-14
    Description: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" 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/PMC3207357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindblad-Toh, Kerstin -- Garber, Manuel -- Zuk, Or -- Lin, Michael F -- Parker, Brian J -- Washietl, Stefan -- Kheradpour, Pouya -- Ernst, Jason -- Jordan, Gregory -- Mauceli, Evan -- Ward, Lucas D -- Lowe, Craig B -- Holloway, Alisha K -- Clamp, Michele -- Gnerre, Sante -- Alfoldi, Jessica -- Beal, Kathryn -- Chang, Jean -- Clawson, Hiram -- Cuff, James -- Di Palma, Federica -- Fitzgerald, Stephen -- Flicek, Paul -- Guttman, Mitchell -- Hubisz, Melissa J -- Jaffe, David B -- Jungreis, Irwin -- Kent, W James -- Kostka, Dennis -- Lara, Marcia -- Martins, Andre L -- Massingham, Tim -- Moltke, Ida -- Raney, Brian J -- Rasmussen, Matthew D -- Robinson, Jim -- Stark, Alexander -- Vilella, Albert J -- Wen, Jiayu -- Xie, Xiaohui -- Zody, Michael C -- Broad Institute Sequencing Platform and Whole Genome Assembly Team -- Baldwin, Jen -- Bloom, Toby -- Chin, Chee Whye -- Heiman, Dave -- Nicol, Robert -- Nusbaum, Chad -- Young, Sarah -- Wilkinson, Jane -- Worley, Kim C -- Kovar, Christie L -- Muzny, Donna M -- Gibbs, Richard A -- Baylor College of Medicine Human Genome Sequencing Center Sequencing Team -- Cree, Andrew -- Dihn, Huyen H -- Fowler, Gerald -- Jhangiani, Shalili -- Joshi, Vandita -- Lee, Sandra -- Lewis, Lora R -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Santibanez, Jireh -- Warren, Wesley C -- Mardis, Elaine R -- Weinstock, George M -- Wilson, Richard K -- Genome Institute at Washington University -- Delehaunty, Kim -- Dooling, David -- Fronik, Catrina -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Minx, Patrick -- Sodergren, Erica -- Birney, Ewan -- Margulies, Elliott H -- Herrero, Javier -- Green, Eric D -- Haussler, David -- Siepel, Adam -- Goldman, Nick -- Pollard, Katherine S -- Pedersen, Jakob S -- Lander, Eric S -- Kellis, Manolis -- 095908/Wellcome Trust/United Kingdom -- GM82901/GM/NIGMS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-09/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. kersli@broadinstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993624" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Disease ; *Evolution, Molecular ; Exons/genetics ; Genome/*genetics ; Genome, Human/*genetics ; Genomics ; Health ; Humans ; Mammals/*genetics ; Molecular Sequence Annotation ; Phylogeny ; RNA/classification/genetics ; Selection, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA
    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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  • 8
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    Comparative and demographic analysis of orang-utan genomes (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-01-29
    Description: 'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778/" 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/PMC3060778/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Locke, Devin P -- Hillier, LaDeana W -- Warren, Wesley C -- Worley, Kim C -- Nazareth, Lynne V -- Muzny, Donna M -- Yang, Shiaw-Pyng -- Wang, Zhengyuan -- Chinwalla, Asif T -- Minx, Pat -- Mitreva, Makedonka -- Cook, Lisa -- Delehaunty, Kim D -- Fronick, Catrina -- Schmidt, Heather -- Fulton, Lucinda A -- Fulton, Robert S -- Nelson, Joanne O -- Magrini, Vincent -- Pohl, Craig -- Graves, Tina A -- Markovic, Chris -- Cree, Andy -- Dinh, Huyen H -- Hume, Jennifer -- Kovar, Christie L -- Fowler, Gerald R -- Lunter, Gerton -- Meader, Stephen -- Heger, Andreas -- Ponting, Chris P -- Marques-Bonet, Tomas -- Alkan, Can -- Chen, Lin -- Cheng, Ze -- Kidd, Jeffrey M -- Eichler, Evan E -- White, Simon -- Searle, Stephen -- Vilella, Albert J -- Chen, Yuan -- Flicek, Paul -- Ma, Jian -- Raney, Brian -- Suh, Bernard -- Burhans, Richard -- Herrero, Javier -- Haussler, David -- Faria, Rui -- Fernando, Olga -- Darre, Fleur -- Farre, Domenec -- Gazave, Elodie -- Oliva, Meritxell -- Navarro, Arcadi -- Roberto, Roberta -- Capozzi, Oronzo -- Archidiacono, Nicoletta -- Della Valle, Giuliano -- Purgato, Stefania -- Rocchi, Mariano -- Konkel, Miriam K -- Walker, Jerilyn A -- Ullmer, Brygg -- Batzer, Mark A -- Smit, Arian F A -- Hubley, Robert -- Casola, Claudio -- Schrider, Daniel R -- Hahn, Matthew W -- Quesada, Victor -- Puente, Xose S -- Ordonez, Gonzalo R -- Lopez-Otin, Carlos -- Vinar, Tomas -- Brejova, Brona -- Ratan, Aakrosh -- Harris, Robert S -- Miller, Webb -- Kosiol, Carolin -- Lawson, Heather A -- Taliwal, Vikas -- Martins, Andre L -- Siepel, Adam -- Roychoudhury, Arindam -- Ma, Xin -- Degenhardt, Jeremiah -- Bustamante, Carlos D -- Gutenkunst, Ryan N -- Mailund, Thomas -- Dutheil, Julien Y -- Hobolth, Asger -- Schierup, Mikkel H -- Ryder, Oliver A -- Yoshinaga, Yuko -- de Jong, Pieter J -- Weinstock, George M -- Rogers, Jeffrey -- Mardis, Elaine R -- Gibbs, Richard A -- Wilson, Richard K -- G0501331/Medical Research Council/United Kingdom -- HG002238/HG/NHGRI NIH HHS/ -- HG002385/HG/NHGRI NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- P01 AG022064/AG/NIA NIH HHS/ -- R01 GM059290/GM/NIGMS NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003079-08/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA. dlocke@wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21270892" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Centromere/genetics ; Cerebrosides/metabolism ; Chromosomes ; Evolution, Molecular ; Female ; Gene Rearrangement/genetics ; Genetic Speciation ; *Genetic Variation ; Genetics, Population ; Genome/*genetics ; Humans ; Male ; Phylogeny ; Pongo abelii/*genetics ; Pongo pygmaeus/*genetics ; Population Density ; Population Dynamics ; Species Specificity
    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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  • 9
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    Elephant shark genome provides unique insights into gnathostome evolution (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-01-10
    Description: The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the 'living fossil' coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964593/" 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/PMC3964593/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venkatesh, Byrappa -- Lee, Alison P -- Ravi, Vydianathan -- Maurya, Ashish K -- Lian, Michelle M -- Swann, Jeremy B -- Ohta, Yuko -- Flajnik, Martin F -- Sutoh, Yoichi -- Kasahara, Masanori -- Hoon, Shawn -- Gangu, Vamshidhar -- Roy, Scott W -- Irimia, Manuel -- Korzh, Vladimir -- Kondrychyn, Igor -- Lim, Zhi Wei -- Tay, Boon-Hui -- Tohari, Sumanty -- Kong, Kiat Whye -- Ho, Shufen -- Lorente-Galdos, Belen -- Quilez, Javier -- Marques-Bonet, Tomas -- Raney, Brian J -- Ingham, Philip W -- Tay, Alice -- Hillier, LaDeana W -- Minx, Patrick -- Boehm, Thomas -- Wilson, Richard K -- Brenner, Sydney -- Warren, Wesley C -- AI27877/AI/NIAID NIH HHS/ -- R01 AI027877/AI/NIAID NIH HHS/ -- R01 OD010549/OD/NIH HHS/ -- RR006603/RR/NCRR NIH HHS/ -- U41 HG002371/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Jan 9;505(7482):174-9. doi: 10.1038/nature12826.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673 [2] Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228. ; Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673. ; Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673. ; Department of Developmental Immunology, Max-Planck-Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany. ; Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland 21201, USA. ; Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan. ; Molecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673. ; Department of Biology, San Francisco State University, San Francisco, California 94132, USA. ; Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ; Fish Developmental Biology Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673. ; 1] Institut de Biologia Evolutiva (UPF-CSIC), PRBB, 08003 Barcelona, Spain [2] Institucio Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Catalonia, Spain. ; Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA. ; The Genome Institute at Washington University, St Louis, Missouri 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24402279" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Cell Lineage/immunology ; *Evolution, Molecular ; Fish Proteins/classification/genetics ; Gene Deletion ; Genome/*genetics ; Genomics ; Immunity, Cellular/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Osteogenesis/genetics ; Phosphoproteins/genetics/metabolism ; Phylogeny ; Protein Structure, Tertiary/genetics ; Sharks/*genetics/immunology ; T-Lymphocytes/cytology/immunology ; Time Factors ; Vertebrates/classification/genetics ; Zebrafish/genetics/growth & development
    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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  • 10
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    A catalog of reference genomes from the human microbiome (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    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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