ALBERT

Description: Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holt, Robert A -- Subramanian, G Mani -- Halpern, Aaron -- Sutton, Granger G -- Charlab, Rosane -- Nusskern, Deborah R -- Wincker, Patrick -- Clark, Andrew G -- Ribeiro, Jose M C -- Wides, Ron -- Salzberg, Steven L -- Loftus, Brendan -- Yandell, Mark -- Majoros, William H -- Rusch, Douglas B -- Lai, Zhongwu -- Kraft, Cheryl L -- Abril, Josep F -- Anthouard, Veronique -- Arensburger, Peter -- Atkinson, Peter W -- Baden, Holly -- de Berardinis, Veronique -- Baldwin, Danita -- Benes, Vladimir -- Biedler, Jim -- Blass, Claudia -- Bolanos, Randall -- Boscus, Didier -- Barnstead, Mary -- Cai, Shuang -- Center, Angela -- Chaturverdi, Kabir -- Christophides, George K -- Chrystal, Mathew A -- Clamp, Michele -- Cravchik, Anibal -- Curwen, Val -- Dana, Ali -- Delcher, Art -- Dew, Ian -- Evans, Cheryl A -- Flanigan, Michael -- Grundschober-Freimoser, Anne -- Friedli, Lisa -- Gu, Zhiping -- Guan, Ping -- Guigo, Roderic -- Hillenmeyer, Maureen E -- Hladun, Susanne L -- Hogan, James R -- Hong, Young S -- Hoover, Jeffrey -- Jaillon, Olivier -- Ke, Zhaoxi -- Kodira, Chinnappa -- Kokoza, Elena -- Koutsos, Anastasios -- Letunic, Ivica -- Levitsky, Alex -- Liang, Yong -- Lin, Jhy-Jhu -- Lobo, Neil F -- Lopez, John R -- Malek, Joel A -- McIntosh, Tina C -- Meister, Stephan -- Miller, Jason -- Mobarry, Clark -- Mongin, Emmanuel -- Murphy, Sean D -- O'Brochta, David A -- Pfannkoch, Cynthia -- Qi, Rong -- Regier, Megan A -- Remington, Karin -- Shao, Hongguang -- Sharakhova, Maria V -- Sitter, Cynthia D -- Shetty, Jyoti -- Smith, Thomas J -- Strong, Renee -- Sun, Jingtao -- Thomasova, Dana -- Ton, Lucas Q -- Topalis, Pantelis -- Tu, Zhijian -- Unger, Maria F -- Walenz, Brian -- Wang, Aihui -- Wang, Jian -- Wang, Mei -- Wang, Xuelan -- Woodford, Kerry J -- Wortman, Jennifer R -- Wu, Martin -- Yao, Alison -- Zdobnov, Evgeny M -- Zhang, Hongyu -- Zhao, Qi -- Zhao, Shaying -- Zhu, Shiaoping C -- Zhimulev, Igor -- Coluzzi, Mario -- della Torre, Alessandra -- Roth, Charles W -- Louis, Christos -- Kalush, Francis -- Mural, Richard J -- Myers, Eugene W -- Adams, Mark D -- Smith, Hamilton O -- Broder, Samuel -- Gardner, Malcolm J -- Fraser, Claire M -- Birney, Ewan -- Bork, Peer -- Brey, Paul T -- Venter, J Craig -- Weissenbach, Jean -- Kafatos, Fotis C -- Collins, Frank H -- Hoffman, Stephen L -- R01AI44273/AI/NIAID NIH HHS/ -- U01AI48846/AI/NIAID NIH HHS/ -- U01AI50687/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2002 Oct 4;298(5591):129-49.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA. robert.holt@celera.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12364791" target="_blank"〉PubMed〈/a〉

Description: The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735092/" 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/PMC2735092/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bovine HapMap Consortium -- Gibbs, Richard A -- Taylor, Jeremy F -- Van Tassell, Curtis P -- Barendse, William -- Eversole, Kellye A -- Gill, Clare A -- Green, Ronnie D -- Hamernik, Debora L -- Kappes, Steven M -- Lien, Sigbjorn -- Matukumalli, Lakshmi K -- McEwan, John C -- Nazareth, Lynne V -- Schnabel, Robert D -- Weinstock, George M -- Wheeler, David A -- Ajmone-Marsan, Paolo -- Boettcher, Paul J -- Caetano, Alexandre R -- Garcia, Jose Fernando -- Hanotte, Olivier -- Mariani, Paola -- Skow, Loren C -- Sonstegard, Tad S -- Williams, John L -- Diallo, Boubacar -- Hailemariam, Lemecha -- Martinez, Mario L -- Morris, Chris A -- Silva, Luiz O C -- Spelman, Richard J -- Mulatu, Woudyalew -- Zhao, Keyan -- Abbey, Colette A -- Agaba, Morris -- Araujo, Flabio R -- Bunch, Rowan J -- Burton, James -- Gorni, Chiara -- Olivier, Hanotte -- Harrison, Blair E -- Luff, Bill -- Machado, Marco A -- Mwakaya, Joel -- Plastow, Graham -- Sim, Warren -- Smith, Timothy -- Thomas, Merle B -- Valentini, Alessio -- Williams, Paul -- Womack, James -- Woolliams, John A -- Liu, Yue -- Qin, Xiang -- Worley, Kim C -- Gao, Chuan -- Jiang, Huaiyang -- Moore, Stephen S -- Ren, Yanru -- Song, Xing-Zhi -- Bustamante, Carlos D -- Hernandez, Ryan D -- Muzny, Donna M -- Patil, Shobha -- San Lucas, Anthony -- Fu, Qing -- Kent, Matthew P -- Vega, Richard -- Matukumalli, Aruna -- McWilliam, Sean -- Sclep, Gert -- Bryc, Katarzyna -- Choi, Jungwoo -- Gao, Hong -- Grefenstette, John J -- Murdoch, Brenda -- Stella, Alessandra -- Villa-Angulo, Rafael -- Wright, Mark -- Aerts, Jan -- Jann, Oliver -- Negrini, Riccardo -- Goddard, Mike E -- Hayes, Ben J -- Bradley, Daniel G -- Barbosa da Silva, Marcos -- Lau, Lilian P L -- Liu, George E -- Lynn, David J -- Panzitta, Francesca -- Dodds, Ken G -- R01 GM083606/GM/NIGMS NIH HHS/ -- R01 GM083606-02/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 24;324(5926):528-32. doi: 10.1126/science.1167936.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19390050" target="_blank"〉PubMed〈/a〉

Description: DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882961/" 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/PMC2882961/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scherer, Stephen W -- Cheung, Joseph -- MacDonald, Jeffrey R -- Osborne, Lucy R -- Nakabayashi, Kazuhiko -- Herbrick, Jo-Anne -- Carson, Andrew R -- Parker-Katiraee, Layla -- Skaug, Jennifer -- Khaja, Razi -- Zhang, Junjun -- Hudek, Alexander K -- Li, Martin -- Haddad, May -- Duggan, Gavin E -- Fernandez, Bridget A -- Kanematsu, Emiko -- Gentles, Simone -- Christopoulos, Constantine C -- Choufani, Sanaa -- Kwasnicka, Dorota -- Zheng, Xiangqun H -- Lai, Zhongwu -- Nusskern, Deborah -- Zhang, Qing -- Gu, Zhiping -- Lu, Fu -- Zeesman, Susan -- Nowaczyk, Malgorzata J -- Teshima, Ikuko -- Chitayat, David -- Shuman, Cheryl -- Weksberg, Rosanna -- Zackai, Elaine H -- Grebe, Theresa A -- Cox, Sarah R -- Kirkpatrick, Susan J -- Rahman, Nazneen -- Friedman, Jan M -- Heng, Henry H Q -- Pelicci, Pier Giuseppe -- Lo-Coco, Francesco -- Belloni, Elena -- Shaffer, Lisa G -- Pober, Barbara -- Morton, Cynthia C -- Gusella, James F -- Bruns, Gail A P -- Korf, Bruce R -- Quade, Bradley J -- Ligon, Azra H -- Ferguson, Heather -- Higgins, Anne W -- Leach, Natalia T -- Herrick, Steven R -- Lemyre, Emmanuelle -- Farra, Chantal G -- Kim, Hyung-Goo -- Summers, Anne M -- Gripp, Karen W -- Roberts, Wendy -- Szatmari, Peter -- Winsor, Elizabeth J T -- Grzeschik, Karl-Heinz -- Teebi, Ahmed -- Minassian, Berge A -- Kere, Juha -- Armengol, Lluis -- Pujana, Miguel Angel -- Estivill, Xavier -- Wilson, Michael D -- Koop, Ben F -- Tosi, Sabrina -- Moore, Gudrun E -- Boright, Andrew P -- Zlotorynski, Eitan -- Kerem, Batsheva -- Kroisel, Peter M -- Petek, Erwin -- Oscier, David G -- Mould, Sarah J -- Dohner, Hartmut -- Dohner, Konstanze -- Rommens, Johanna M -- Vincent, John B -- Venter, J Craig -- Li, Peter W -- Mural, Richard J -- Adams, Mark D -- Tsui, Lap-Chee -- 38103/Canadian Institutes of Health Research/Canada -- P01 GM061354/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 May 2;300(5620):767-72. Epub 2003 Apr 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8. steve@genet.sickkids.on.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12690205" target="_blank"〉PubMed〈/a〉

Description: Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078/" 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/PMC4390078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guojie -- Li, Cai -- Li, Qiye -- Li, Bo -- Larkin, Denis M -- Lee, Chul -- Storz, Jay F -- Antunes, Agostinho -- Greenwold, Matthew J -- Meredith, Robert W -- Odeen, Anders -- Cui, Jie -- Zhou, Qi -- Xu, Luohao -- Pan, Hailin -- Wang, Zongji -- Jin, Lijun -- Zhang, Pei -- Hu, Haofu -- Yang, Wei -- Hu, Jiang -- Xiao, Jin -- Yang, Zhikai -- Liu, Yang -- Xie, Qiaolin -- Yu, Hao -- Lian, Jinmin -- Wen, Ping -- Zhang, Fang -- Li, Hui -- Zeng, Yongli -- Xiong, Zijun -- Liu, Shiping -- Zhou, Long -- Huang, Zhiyong -- An, Na -- Wang, Jie -- Zheng, Qiumei -- Xiong, Yingqi -- Wang, Guangbiao -- Wang, Bo -- Wang, Jingjing -- Fan, Yu -- da Fonseca, Rute R -- Alfaro-Nunez, Alonzo -- Schubert, Mikkel -- Orlando, Ludovic -- Mourier, Tobias -- Howard, Jason T -- Ganapathy, Ganeshkumar -- Pfenning, Andreas -- Whitney, Osceola -- Rivas, Miriam V -- Hara, Erina -- Smith, Julia -- Farre, Marta -- Narayan, Jitendra -- Slavov, Gancho -- Romanov, Michael N -- Borges, Rui -- Machado, Joao Paulo -- Khan, Imran -- Springer, Mark S -- Gatesy, John -- Hoffmann, Federico G -- Opazo, Juan C -- Hastad, Olle -- Sawyer, Roger H -- Kim, Heebal -- Kim, Kyu-Won -- Kim, Hyeon Jeong -- Cho, Seoae -- Li, Ning -- Huang, Yinhua -- Bruford, Michael W -- Zhan, Xiangjiang -- Dixon, Andrew -- Bertelsen, Mads F -- Derryberry, Elizabeth -- Warren, Wesley -- Wilson, Richard K -- Li, Shengbin -- Ray, David A -- Green, Richard E -- O'Brien, Stephen J -- Griffin, Darren -- Johnson, Warren E -- Haussler, David -- Ryder, Oliver A -- Willerslev, Eske -- Graves, Gary R -- Alstrom, Per -- Fjeldsa, Jon -- Mindell, David P -- Edwards, Scott V -- Braun, Edward L -- Rahbek, Carsten -- Burt, David W -- Houde, Peter -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Avian Genome Consortium -- Jarvis, Erich D -- Gilbert, M Thomas P -- Wang, Jun -- DP1 OD000448/OD/NIH HHS/ -- DP1OD000448/OD/NIH HHS/ -- R01 HL087216/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. ; Royal Veterinary College, University of London, London, UK. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. ; School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA. ; Centro de Investigacion en Ciencias del Mar y Limnologia (CIMAR)/Centro Interdisciplinar de Investigacao Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciencias, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal. ; Department of Biological Sciences, University of South Carolina, Columbia, SC, USA. ; Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA. ; Department of Animal Ecology, Uppsala University, Norbyvagen 18D, S-752 36 Uppsala, Sweden. ; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia. Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore. ; Department of Integrative Biology University of California, Berkeley, CA 94720, USA. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. College of Life Sciences, Wuhan University, Wuhan 430072, China. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. BGI Education Center,University of Chinese Academy of Sciences,Shenzhen, 518083, China. ; Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. ; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK. ; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. ; Centro de Investigacion en Ciencias del Mar y Limnologia (CIMAR)/Centro Interdisciplinar de Investigacao Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Instituto de Ciencias Biomedicas Abel Salazar (ICBAS), Universidade do Porto, Portugal. ; Department of Biology, University of California Riverside, Riverside, CA 92521, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. ; Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Post Office Box 7011, S-750 07, Uppsala, Sweden. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. ; Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. College of Animal Science and Technology, China Agricultural University, Beijing 100094, China. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 China. ; International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK. ; Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark. ; Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA. Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA. ; The Genome Institute at Washington University, St. Louis, MO 63108, USA. ; College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia. Nova Southeastern University Oceanographic Center 8000 N Ocean Drive, Dania, FL 33004, USA. ; Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA. ; Genetics Division, San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA. ; Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Post Office Box 37012, Washington, DC 20013-7012, USA. Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden. ; Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA. ; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Imperial College London, Grand Challenges in Ecosystems and the Environment Initiative, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK. ; Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK. ; Department of Biology, New Mexico State University, Box 30001 MSC 3AF, Las Cruces, NM 88003, USA. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. ; Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504712" target="_blank"〉PubMed〈/a〉

Description: Because of its requirement for signaling by multiple cytokines, Janus kinase 3 (JAK3) is an excellent target for clinical immunosuppression. We report the development of a specific, orally active inhibitor of JAK3, CP-690,550, that significantly prolonged survival in a murine model of heart transplantation and in cynomolgus monkeys receiving kidney transplants. CP-690,550 treatment was not associated with hypertension, hyperlipidemia, or lymphoproliferative disease. On the basis of these preclinical results, we believe JAK3 blockade by CP-690,550 has potential for therapeutically desirable immunosuppression in human organ transplantation and in other clinical settings.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Changelian, Paul S -- Flanagan, Mark E -- Ball, Douglas J -- Kent, Craig R -- Magnuson, Kelly S -- Martin, William H -- Rizzuti, Bonnie J -- Sawyer, Perry S -- Perry, Bret D -- Brissette, William H -- McCurdy, Sandra P -- Kudlacz, Elizabeth M -- Conklyn, Maryrose J -- Elliott, Eileen A -- Koslov, Erika R -- Fisher, Michael B -- Strelevitz, Timothy J -- Yoon, Kwansik -- Whipple, David A -- Sun, Jianmin -- Munchhof, Michael J -- Doty, John L -- Casavant, Jeffrey M -- Blumenkopf, Todd A -- Hines, Michael -- Brown, Matthew F -- Lillie, Brett M -- Subramanyam, Chakrapani -- Shang-Poa, Chang -- Milici, Anthony J -- Beckius, Gretchen E -- Moyer, James D -- Su, Chunyan -- Woodworth, Thasia G -- Gaweco, Anderson S -- Beals, Chan R -- Littman, Bruce H -- Fisher, Douglas A -- Smith, James F -- Zagouras, Panayiotis -- Magna, Holly A -- Saltarelli, Mary J -- Johnson, Kimberly S -- Nelms, Linda F -- Des Etages, Shelley G -- Hayes, Lisa S -- Kawabata, Thomas T -- Finco-Kent, Deborah -- Baker, Deanna L -- Larson, Michael -- Si, Ming-Sing -- Paniagua, Ricardo -- Higgins, John -- Holm, Bari -- Reitz, Bruce -- Zhou, Yong-Jie -- Morris, Randall E -- O'Shea, John J -- Borie, Dominic C -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):875-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immunology Group, Department of Antibacterials and Immunology, Pfizer Global Researchand Development, Groton, CT 06340, USA. paul_s_changelian@groton.pfizer.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593182" target="_blank"〉PubMed〈/a〉

Description: We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569/" 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/PMC3142569/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerstein, Mark B -- Lu, Zhi John -- Van Nostrand, Eric L -- Cheng, Chao -- Arshinoff, Bradley I -- Liu, Tao -- Yip, Kevin Y -- Robilotto, Rebecca -- Rechtsteiner, Andreas -- Ikegami, Kohta -- Alves, Pedro -- Chateigner, Aurelien -- Perry, Marc -- Morris, Mitzi -- Auerbach, Raymond K -- Feng, Xin -- Leng, Jing -- Vielle, Anne -- Niu, Wei -- Rhrissorrakrai, Kahn -- Agarwal, Ashish -- Alexander, Roger P -- Barber, Galt -- Brdlik, Cathleen M -- Brennan, Jennifer -- Brouillet, Jeremy Jean -- Carr, Adrian -- Cheung, Ming-Sin -- Clawson, Hiram -- Contrino, Sergio -- Dannenberg, Luke O -- Dernburg, Abby F -- Desai, Arshad -- Dick, Lindsay -- Dose, Andrea C -- Du, Jiang -- Egelhofer, Thea -- Ercan, Sevinc -- Euskirchen, Ghia -- Ewing, Brent -- Feingold, Elise A -- Gassmann, Reto -- Good, Peter J -- Green, Phil -- Gullier, Francois -- Gutwein, Michelle -- Guyer, Mark S -- Habegger, Lukas -- Han, Ting -- Henikoff, Jorja G -- Henz, Stefan R -- Hinrichs, Angie -- Holster, Heather -- Hyman, Tony -- Iniguez, A Leo -- Janette, Judith -- Jensen, Morten -- Kato, Masaomi -- Kent, W James -- Kephart, Ellen -- Khivansara, Vishal -- Khurana, Ekta -- Kim, John K -- Kolasinska-Zwierz, Paulina -- Lai, Eric C -- Latorre, Isabel -- Leahey, Amber -- Lewis, Suzanna -- Lloyd, Paul -- Lochovsky, Lucas -- Lowdon, Rebecca F -- Lubling, Yaniv -- Lyne, Rachel -- MacCoss, Michael -- Mackowiak, Sebastian D -- Mangone, Marco -- McKay, Sheldon -- Mecenas, Desirea -- Merrihew, Gennifer -- Miller, David M 3rd -- Muroyama, Andrew -- Murray, John I -- Ooi, Siew-Loon -- Pham, Hoang -- Phippen, Taryn -- Preston, Elicia A -- Rajewsky, Nikolaus -- Ratsch, Gunnar -- Rosenbaum, Heidi -- Rozowsky, Joel -- Rutherford, Kim -- Ruzanov, Peter -- Sarov, Mihail -- Sasidharan, Rajkumar -- Sboner, Andrea -- Scheid, Paul -- Segal, Eran -- Shin, Hyunjin -- Shou, Chong -- Slack, Frank J -- Slightam, Cindie -- Smith, Richard -- Spencer, William C -- Stinson, E O -- Taing, Scott -- Takasaki, Teruaki -- Vafeados, Dionne -- Voronina, Ksenia -- Wang, Guilin -- Washington, Nicole L -- Whittle, Christina M -- Wu, Beijing -- Yan, Koon-Kiu -- Zeller, Georg -- Zha, Zheng -- Zhong, Mei -- Zhou, Xingliang -- modENCODE Consortium -- Ahringer, Julie -- Strome, Susan -- Gunsalus, Kristin C -- Micklem, Gos -- Liu, X Shirley -- Reinke, Valerie -- Kim, Stuart K -- Hillier, LaDeana W -- Henikoff, Steven -- Piano, Fabio -- Snyder, Michael -- Stein, Lincoln -- Lieb, Jason D -- Waterston, Robert H -- 054523/Wellcome Trust/United Kingdom -- R01 GM088565/GM/NIGMS NIH HHS/ -- R01 GM088565-03/GM/NIGMS NIH HHS/ -- R01GM088565/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA. modencode.worm.pi@gersteinlab.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177976" target="_blank"〉PubMed〈/a〉

Description: African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berriman, Matthew -- Ghedin, Elodie -- Hertz-Fowler, Christiane -- Blandin, Gaelle -- Renauld, Hubert -- Bartholomeu, Daniella C -- Lennard, Nicola J -- Caler, Elisabet -- Hamlin, Nancy E -- Haas, Brian -- Bohme, Ulrike -- Hannick, Linda -- Aslett, Martin A -- Shallom, Joshua -- Marcello, Lucio -- Hou, Lihua -- Wickstead, Bill -- Alsmark, U Cecilia M -- Arrowsmith, Claire -- Atkin, Rebecca J -- Barron, Andrew J -- Bringaud, Frederic -- Brooks, Karen -- Carrington, Mark -- Cherevach, Inna -- Chillingworth, Tracey-Jane -- Churcher, Carol -- Clark, Louise N -- Corton, Craig H -- Cronin, Ann -- Davies, Rob M -- Doggett, Jonathon -- Djikeng, Appolinaire -- Feldblyum, Tamara -- Field, Mark C -- Fraser, Audrey -- Goodhead, Ian -- Hance, Zahra -- Harper, David -- Harris, Barbara R -- Hauser, Heidi -- Hostetler, Jessica -- Ivens, Al -- Jagels, Kay -- Johnson, David -- Johnson, Justin -- Jones, Kristine -- Kerhornou, Arnaud X -- Koo, Hean -- Larke, Natasha -- Landfear, Scott -- Larkin, Christopher -- Leech, Vanessa -- Line, Alexandra -- Lord, Angela -- Macleod, Annette -- Mooney, Paul J -- Moule, Sharon -- Martin, David M A -- Morgan, Gareth W -- Mungall, Karen -- Norbertczak, Halina -- Ormond, Doug -- Pai, Grace -- Peacock, Chris S -- Peterson, Jeremy -- Quail, Michael A -- Rabbinowitsch, Ester -- Rajandream, Marie-Adele -- Reitter, Chris -- Salzberg, Steven L -- Sanders, Mandy -- Schobel, Seth -- Sharp, Sarah -- Simmonds, Mark -- Simpson, Anjana J -- Tallon, Luke -- Turner, C Michael R -- Tait, Andrew -- Tivey, Adrian R -- Van Aken, Susan -- Walker, Danielle -- Wanless, David -- Wang, Shiliang -- White, Brian -- White, Owen -- Whitehead, Sally -- Woodward, John -- Wortman, Jennifer -- Adams, Mark D -- Embley, T Martin -- Gull, Keith -- Ullu, Elisabetta -- Barry, J David -- Fairlamb, Alan H -- Opperdoes, Fred -- Barrell, Barclay G -- Donelson, John E -- Hall, Neil -- Fraser, Claire M -- Melville, Sara E -- El-Sayed, Najib M -- AI43062/AI/NIAID NIH HHS/ -- R01 AI043062/AI/NIAID NIH HHS/ -- U01 AI043062/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):416-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. mb4@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020726" target="_blank"〉PubMed〈/a〉

Description: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199/" 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/PMC3529199/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Colbourne, John K -- Pfrender, Michael E -- Gilbert, Donald -- Thomas, W Kelley -- Tucker, Abraham -- Oakley, Todd H -- Tokishita, Shinichi -- Aerts, Andrea -- Arnold, Georg J -- Basu, Malay Kumar -- Bauer, Darren J -- Caceres, Carla E -- Carmel, Liran -- Casola, Claudio -- Choi, Jeong-Hyeon -- Detter, John C -- Dong, Qunfeng -- Dusheyko, Serge -- Eads, Brian D -- Frohlich, Thomas -- Geiler-Samerotte, Kerry A -- Gerlach, Daniel -- Hatcher, Phil -- Jogdeo, Sanjuro -- Krijgsveld, Jeroen -- Kriventseva, Evgenia V -- Kultz, Dietmar -- Laforsch, Christian -- Lindquist, Erika -- Lopez, Jacqueline -- Manak, J Robert -- Muller, Jean -- Pangilinan, Jasmyn -- Patwardhan, Rupali P -- Pitluck, Samuel -- Pritham, Ellen J -- Rechtsteiner, Andreas -- Rho, Mina -- Rogozin, Igor B -- Sakarya, Onur -- Salamov, Asaf -- Schaack, Sarah -- Shapiro, Harris -- Shiga, Yasuhiro -- Skalitzky, Courtney -- Smith, Zachary -- Souvorov, Alexander -- Sung, Way -- Tang, Zuojian -- Tsuchiya, Dai -- Tu, Hank -- Vos, Harmjan -- Wang, Mei -- Wolf, Yuri I -- Yamagata, Hideo -- Yamada, Takuji -- Ye, Yuzhen -- Shaw, Joseph R -- Andrews, Justen -- Crease, Teresa J -- Tang, Haixu -- Lucas, Susan M -- Robertson, Hugh M -- Bork, Peer -- Koonin, Eugene V -- Zdobnov, Evgeny M -- Grigoriev, Igor V -- Lynch, Michael -- Boore, Jeffrey L -- P42 ES004699/ES/NIEHS NIH HHS/ -- P42 ES004699-25/ES/NIEHS NIH HHS/ -- P42ES004699/ES/NIEHS NIH HHS/ -- R01 ES019324/ES/NIEHS NIH HHS/ -- R24 GM078274/GM/NIGMS NIH HHS/ -- R24 GM078274-01A1/GM/NIGMS NIH HHS/ -- R24GM07827401/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA. jcolbour@indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292972" target="_blank"〉PubMed〈/a〉

Description: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" 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/PMC2875087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merchant, Sabeeha S -- Prochnik, Simon E -- Vallon, Olivier -- Harris, Elizabeth H -- Karpowicz, Steven J -- Witman, George B -- Terry, Astrid -- Salamov, Asaf -- Fritz-Laylin, Lillian K -- Marechal-Drouard, Laurence -- Marshall, Wallace F -- Qu, Liang-Hu -- Nelson, David R -- Sanderfoot, Anton A -- Spalding, Martin H -- Kapitonov, Vladimir V -- Ren, Qinghu -- Ferris, Patrick -- Lindquist, Erika -- Shapiro, Harris -- Lucas, Susan M -- Grimwood, Jane -- Schmutz, Jeremy -- Cardol, Pierre -- Cerutti, Heriberto -- Chanfreau, Guillaume -- Chen, Chun-Long -- Cognat, Valerie -- Croft, Martin T -- Dent, Rachel -- Dutcher, Susan -- Fernandez, Emilio -- Fukuzawa, Hideya -- Gonzalez-Ballester, David -- Gonzalez-Halphen, Diego -- Hallmann, Armin -- Hanikenne, Marc -- Hippler, Michael -- Inwood, William -- Jabbari, Kamel -- Kalanon, Ming -- Kuras, Richard -- Lefebvre, Paul A -- Lemaire, Stephane D -- Lobanov, Alexey V -- Lohr, Martin -- Manuell, Andrea -- Meier, Iris -- Mets, Laurens -- Mittag, Maria -- Mittelmeier, Telsa -- Moroney, James V -- Moseley, Jeffrey -- Napoli, Carolyn -- Nedelcu, Aurora M -- Niyogi, Krishna -- Novoselov, Sergey V -- Paulsen, Ian T -- Pazour, Greg -- Purton, Saul -- Ral, Jean-Philippe -- Riano-Pachon, Diego Mauricio -- Riekhof, Wayne -- Rymarquis, Linda -- Schroda, Michael -- Stern, David -- Umen, James -- Willows, Robert -- Wilson, Nedra -- Zimmer, Sara Lana -- Allmer, Jens -- Balk, Janneke -- Bisova, Katerina -- Chen, Chong-Jian -- Elias, Marek -- Gendler, Karla -- Hauser, Charles -- Lamb, Mary Rose -- Ledford, Heidi -- Long, Joanne C -- Minagawa, Jun -- Page, M Dudley -- Pan, Junmin -- Pootakham, Wirulda -- Roje, Sanja -- Rose, Annkatrin -- Stahlberg, Eric -- Terauchi, Aimee M -- Yang, Pinfen -- Ball, Steven -- Bowler, Chris -- Dieckmann, Carol L -- Gladyshev, Vadim N -- Green, Pamela -- Jorgensen, Richard -- Mayfield, Stephen -- Mueller-Roeber, Bernd -- Rajamani, Sathish -- Sayre, Richard T -- Brokstein, Peter -- Dubchak, Inna -- Goodstein, David -- Hornick, Leila -- Huang, Y Wayne -- Jhaveri, Jinal -- Luo, Yigong -- Martinez, Diego -- Ngau, Wing Chi Abby -- Otillar, Bobby -- Poliakov, Alexander -- Porter, Aaron -- Szajkowski, Lukasz -- Werner, Gregory -- Zhou, Kemin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Grossman, Arthur R -- GM07185/GM/NIGMS NIH HHS/ -- GM42143/GM/NIGMS NIH HHS/ -- R01 GM032843/GM/NIGMS NIH HHS/ -- R01 GM042143/GM/NIGMS NIH HHS/ -- R01 GM042143-09/GM/NIGMS NIH HHS/ -- R01 GM060992/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- R37 GM030626/GM/NIGMS NIH HHS/ -- R37 GM042143/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):245-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932292" target="_blank"〉PubMed〈/a〉

Description: We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2080659/" 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/PMC2080659/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carlton, Jane M -- Hirt, Robert P -- Silva, Joana C -- Delcher, Arthur L -- Schatz, Michael -- Zhao, Qi -- Wortman, Jennifer R -- Bidwell, Shelby L -- Alsmark, U Cecilia M -- Besteiro, Sebastien -- Sicheritz-Ponten, Thomas -- Noel, Christophe J -- Dacks, Joel B -- Foster, Peter G -- Simillion, Cedric -- Van de Peer, Yves -- Miranda-Saavedra, Diego -- Barton, Geoffrey J -- Westrop, Gareth D -- Muller, Sylke -- Dessi, Daniele -- Fiori, Pier Luigi -- Ren, Qinghu -- Paulsen, Ian -- Zhang, Hanbang -- Bastida-Corcuera, Felix D -- Simoes-Barbosa, Augusto -- Brown, Mark T -- Hayes, Richard D -- Mukherjee, Mandira -- Okumura, Cheryl Y -- Schneider, Rachel -- Smith, Alias J -- Vanacova, Stepanka -- Villalvazo, Maria -- Haas, Brian J -- Pertea, Mihaela -- Feldblyum, Tamara V -- Utterback, Terry R -- Shu, Chung-Li -- Osoegawa, Kazutoyo -- de Jong, Pieter J -- Hrdy, Ivan -- Horvathova, Lenka -- Zubacova, Zuzana -- Dolezal, Pavel -- Malik, Shehre-Banoo -- Logsdon, John M Jr -- Henze, Katrin -- Gupta, Arti -- Wang, Ching C -- Dunne, Rebecca L -- Upcroft, Jacqueline A -- Upcroft, Peter -- White, Owen -- Salzberg, Steven L -- Tang, Petrus -- Chiu, Cheng-Hsun -- Lee, Ying-Shiung -- Embley, T Martin -- Coombs, Graham H -- Mottram, Jeremy C -- Tachezy, Jan -- Fraser-Liggett, Claire M -- Johnson, Patricia J -- 072031/Wellcome Trust/United Kingdom -- G0000508/Medical Research Council/United Kingdom -- G0000508(56841)/Medical Research Council/United Kingdom -- G9722968/Medical Research Council/United Kingdom -- G9722968(65078)/Medical Research Council/United Kingdom -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- R01 LM007938/LM/NLM NIH HHS/ -- R01 LM007938-04/LM/NLM NIH HHS/ -- U01 AI050913/AI/NIAID NIH HHS/ -- U01 AI050913-01A1/AI/NIAID NIH HHS/ -- U01 AI050913-02/AI/NIAID NIH HHS/ -- UO1 AI50913-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Jan 12;315(5809):207-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Research Drive, Rockville, MD 20850, USA. jane.carlton@med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17218520" target="_blank"〉PubMed〈/a〉