Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970’s Egypt

Autor: de Miranda, JR, Brettell, LE, Chejanovsky, N, Childers, AK, Dalmon, A, Deboutte, W, de Graaf, DC, Doublet, V, Gebremedhn, H, Genersch, E, Gisder, S, Granberg, F, Haddad, NJ, Kaden, R, Manley, R, Matthijnssens, J, Meeus, I, Migdadi, H, Milbrath, MO, Mondet, F, Remnant, EJ, Roberts, JMK, Ryabov, EV, Sela, N, Smagghe, G, Somanathan, H, Wilfert, L, Wright, ON, Martin, SJ, Ball, BV

Publikováno v: VIROLOGY JOURNAL
Virology Journal, Vol 19, Iss 1, Pp 1-11 (2022)
Virology Journal

In 1977, a sample of diseased adult honeybees (Apis mellifera) from Egypt was found to contain large amounts of a previously unknown virus, Egypt bee virus, which was subsequently shown to be serologically related to deformed wing virus (DWV). By seq

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4da475e458c6d28c1a8c032b4cf85f0
https://doi.org/10.1186/s12985-022-01740-2

The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator.

Autor: Pope NS; Department of Entomology, The Pennsylvania State University, University Park, PA 16802.; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403., Singh A; Department of Entomology, The Pennsylvania State University, University Park, PA 16802., Childers AK; Bee Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705., Kapheim KM; Department of Biology, Utah State University, Logan, UT 84322., Evans JD; Bee Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705., López-Uribe MM; Department of Entomology, The Pennsylvania State University, University Park, PA 16802.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2023 Apr 11; Vol. 120 (15), pp. e2208116120. Date of Electronic Publication: 2023 Apr 03.

polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

Autor: Chang J; USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi.; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee.; Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames., Stahlke AR; USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, Beltsville Maryland., Chudalayandi S; Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames., Rosen BD; USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Beltsville, Maryland., Childers AK; USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, Beltsville Maryland., Severin AJ; Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames.

Publikováno v: Genome biology and evolution [Genome Biol Evol] 2023 Mar 03; Vol. 15 (3).

Why sequence all eukaryotes?

Autor: Blaxter M; Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom; mb35@sanger.ac.uk., Archibald JM; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada., Childers AK; Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705., Coddington JA; Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560., Crandall KA; Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052.; Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013., Di Palma F; School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom., Durbin R; Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom., Edwards SV; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138., Graves JAM; School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia.; University of Canberra, Bruce, ACT 2617, Australia., Hackett KJ; Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705., Hall N; Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom., Jarvis ED; Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065.; Howard Hughes Medical Institute, Chevy Chase, MD 20815., Johnson RN; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560., Karlsson EK; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605.; Broad Institute of MIT and Harvard, Cambridge, MA 02142., Kress WJ; Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012., Kuraku S; Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan., Lawniczak MKN; Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom., Lindblad-Toh K; Broad Institute of MIT and Harvard, Cambridge, MA 02142.; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden., Lopez JV; Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004.; Guy Harvey Oceanographic Center, Dania Beach, FL 33004., Moran NA; Integrative Biology, University of Texas at Austin, Austin, TX 78712., Robinson GE; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.; Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801., Ryder OA; Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027.; Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039., Shapiro B; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064., Soltis PS; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611.; Biodiversity Institute, University of Florida, Gainesville, FL 32611., Warnow T; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301., Zhang G; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark.; China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China., Lewin HA; Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616.; Department of Population Health and Reproduction, University of California, Davis, CA 95616.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2022 Jan 25; Vol. 119 (4).

The Earth BioGenome Project 2020: Starting the clock.

Autor: Lewin HA; Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616; lewin@ucdavis.edu.; Department of Population Health and Reproduction, University of California, Davis, CA 95616., Richards S; University of California Davis Genome Center, University of California, Davis, CA 95616., Lieberman Aiden E; DNA Zoo and The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030., Allende ML; Center for Genome Regulation, Universidad de Chile 3425 Santiago, Chile.; Facultad de Ciencias, Universidad de Chile 3425 Santiago, Chile., Archibald JM; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada., Bálint M; LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany.; Institute for Insect Biotechnology, Justus-Liebig University 35392 Giessen, Germany., Barker KB; Global Genome Biodiversity Network Secretariat, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560., Baumgartner B; Revive & Restore, Sausalito, CA 94965., Belov K; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia., Bertorelle G; Department of Life Sciences and Biotechnology, University of Ferrara 44121 Ferrara, Italy., Blaxter ML; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom., Cai J; School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China., Caperello ND; University of California Davis Genome Center, University of California, Davis, CA 95616., Carlson K; The Novim Group, University of California, Santa Barbara, CA 93106., Castilla-Rubio JC; Spacetime Ventures 05449-050 São Paulo, Brazil., Chaw SM; Biodiversity Research Center, Academia Sinica 11529 Taipei, Taiwan., Chen L; School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China., Childers AK; Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705., Coddington JA; Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560., Conde DA; Conservation Science, Species360 Conservation Science Alliance, Bloomington, MN 55425.; Department of Biology, University of Southern Denmark 5230 Odense M, Denmark., Corominas M; Department of Genetics, Microbiology, and Statistics, Universitat de Barcelona 08028 Barcelona, Spain.; Catalan Society for Biology, Institute for Catalan Studies 08001 Barcelona, Spain., Crandall KA; Department of Biostatistics & Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC 20052.; Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052., Crawford AJ; Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia., DiPalma F; Genome British Columbia, Vancouver, BC V5Z 0C4, Canada., Durbin R; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom.; Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom., Ebenezer TE; UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom., Edwards SV; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138., Fedrigo O; Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065., Flicek P; Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom.; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom., Formenti G; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065., Gibbs RA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030., Gilbert MTP; GLOBE Institute, University of Copenhagen 1350 Copenhagen, Denmark.; University Museum, Norwegian University of Science and Technology 7491 Trondheim, Norway., Goldstein MM; Department of Health Policy and Management, George Washington University, Washington, DC 20052., Graves JM; School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia.; Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia., Greely HT; Stanford Law School, Stanford University, Stanford, CA 94305., Grigoriev IV; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720., Hackett KJ; Office of National Programs, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705., Hall N; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom., Haussler D; Genome Institute, University of California, Santa Cruz, CA 95060.; HHMI, Chevy Chase, MD 20815., Helgen KM; Australian Museum Research Institute, Australian Museum, Sydney, NSW 2000, Australia., Hogg CJ; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia., Isobe S; Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan., Jakobsen KS; Department of Biosciences, University of Oslo, Oslo 0316, Norway., Janke A; LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany., Jarvis ED; Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065.; HHMI, Chevy Chase, MD 20815., Johnson WE; Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, MD 20746.; Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630., Jones SJM; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada., Karlsson EK; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605.; Broad Institute of MIT and Harvard, Cambridge, MA 02142., Kersey PJ; Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom., Kim JH; Division of Life Sciences, Korea Polar Research Institute 21990 Incheon, South Korea., Kress WJ; Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012., Kuraku S; Department of Genomics and Evolutionary Biology, National Institute of Genetics 411-8540 Shizuoka, Japan.; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research 650-0047 Hyogo, Japan., Lawniczak MKN; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom., Leebens-Mack JH; Department of Plant Biology, University of Georgia, Athens, GA 30602., Li X; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China., Lindblad-Toh K; Broad Institute of MIT and Harvard, Cambridge, MA 02142.; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 752 36 Uppsala, Sweden., Liu X; BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China., Lopez JV; Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004.; Guy Harvey Oceanographic Center, Dania Beach, FL 33004., Marques-Bonet T; Institute of Evolutionary Biology, Pompeu Fabra University, Consejo Superior de Investigaciones Cientificas, Parc de Recerca Biomedica de Barcelona 08003 Barcelona, Spain.; Catalan Institute of Research and Advanced Studies 08010 Barcelona, Spain.; Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain.; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain., Mazard S; Bioplatforms Australia, Macquarie University, Sydney, NSW 2109, Australia., Mazet JAK; One Health Institute, University of California Davis, CA 95616., Mazzoni CJ; Berlin Center for Genomics in Biodiversity Research 14195 Berlin, Germany.; Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research 10315 Berlin, Germany., Myers EW; Max Planck Institute for Molecular Cell Biology and Genetics 01307 Dresden, Germany., O'Neill RJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269., Paez S; Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065., Park H; Division of Biotechnology, Korea University 02841 Seoul, Korea., Robinson GE; Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801., Roquet C; Systematics and Evolution of Vascular Plants Associated Unit to Consejo Superior de Investigaciones Cientificas, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain.; Laboratoire d'Ecologie Alpine, University Grenoble Alpes, University Savoie Mont Blanc, CNRS 38000 Grenoble, France., Ryder OA; Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027.; Division of Biology, Department of Evolution, Behavior, and Ecology, University of California, San Diego, La Jolla, CA 92039., Sabir JSM; Department of Biological Sciences, Faculty of Science, King Abdulaziz University 21589 Jeddah, Saudi Arabia.; Centre of Excellence in Bionanoscience Research, King Abdulaziz University 21589 Jeddah, Saudi Arabia., Shaffer HB; La Kretz Center for California Conservation Science, Institute of Environment and Sustainability, University of California, Los Angeles, CA 90024.; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095., Shank TM; Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543., Sherkow JS; Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.; College of Law, University of Illinois at Urbana-Champaign, Champaign, IL 61820., Soltis PS; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611.; Biodiversity Institute, University of Florida, Gainesville, FL 32611., Tang B; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University 224002 Yancheng, China., Tedersoo L; Center of Mycology and Microbiology, University of Tartu 50411 Tartu, Estonia.; College of Science, King Saud University 11451 Riyadh, Saudi Arabia., Uliano-Silva M; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom., Wang K; School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China., Wei X; BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China., Wetzer R; Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007.; Biological Sciences, University of Southern California, Los Angeles, CA 90089., Wilson JL; Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom., Xu X; BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China., Yang H; BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China., Yoder AD; Department of Biology, Duke University, Durham, NC 27708.; Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708., Zhang G; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China.; BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China.; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 2100 Copenhagen, Denmark.; China National Genebank, Beijing Genomics Institute 51803 Shenzhen, China.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2022 Jan 25; Vol. 119 (4).