Improved reference genome of Aedes aegypti informs arbovirus vector control

Autor: Adam M. Phillippy, Richard Hall, Michael R. Murphy, Vinita Joardar, Daniel E. Neafsey, Bradley J. White, Margaret Herre, Gareth D. Weedall, Steven D. Buckingham, Louis Lambrechts, Hugh M. Robertson, Andrew K. Jones, David B. Sattelle, Han Cao, Karla Saavedra-Rodriguez, Yang Wu, Maria V. Sharakhova, Allison M Weakley, Atashi Sharma, Alexander S. Raikhel, Olga Dudchenko, Catherine A. Hill, Sourav Roy, Saki Chan, Sara N. Mitchell, Alex Hastie, Arina D. Omer, Igor Filipović, Zhilei Zhao, Raissa G.G. Kay, Melissa Smith, Joyce Lee, Eric Cox, Sergey Koren, Li Zhao, Vidya Ramasamy, Benjamin J. Matthews, Joe Turner, William C. Black, Noah H. Rose, Leslie B. Vosshall, Erez Lieberman Aiden, Corey L. Campbell, Gordana Rašić, Zhijian Tu, J. Spencer Johnston, Jill Muehling, Jonas Korlach, Igor V. Sharakhov, Seth Redmond, Thanyalak Fansiri, Andrea Gloria-Soria, Omar S. Akbari, Aviva Presser Aiden, Richard S. Mann, Igor Antoshechkin, Jacob E. Crawford, Frederick A. Partridge, Alistair C. Darby, Sanjit S. Batra, Carolyn S. McBride, Sarah B. Kingan, Jeffrey R. Powell, Benjamin R. Evans, Gareth J Lycett, William J. Glassford, Paul Peluso, Shruti Sharan, Albin Fontaine, Carlos A Brito-Sierra, Terence Murphy, Vamsi K. Kodali
Přispěvatelé: Rockefeller University [New York], Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC), Kavli Neural Systems Institute, Baylor College of Medicine (BCM), Baylor University, Rice University [Houston], Pacific Biosciences [Menlo Park], Pacific Biosciences of California, National Human Genome Research Institute (NHGRI), California Institute of Technology (CALTECH), Verily Life Sciences Inc, Columbia University [New York], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Harvard T.H. Chan School of Public Health, Princeton University, Liverpool John Moores University (LJMU), Virginia Tech [Blacksburg], Southern Medical University [Guangzhou], Purdue University [West Lafayette], University College of London [London] (UCL), Colorado State University [Fort Collins] (CSU), Bionano Genomics Inc, National Center for Biotechnology Information (NCBI), Yale University [New Haven], Armed Forces Research Institute of Medical Sciences [Bangkok] (AFRIMS), QIMR Berghofer Medical Research Institute, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Oxford Brookes University, University of California [Riverside] (UC Riverside), University of California (UC), Liverpool School of Tropical Medicine (LSTM), University of Liverpool, University of California [San Diego] (UC San Diego), Texas A&M University [College Station], Tomsk State University [Tomsk], University of Illinois [Chicago] (UIC), University of Illinois System, Howard Hughes Medical Institute [New York], This research was supported in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under grant number U19AI110818 to the Broad Institute (S.N.R. and D.E.N.), USDA 2017-05741 (E.L.A.), NSF PHY-1427654 Center for Theoretical Biological Physics (E.L.A.), NIH Intramural Research Program, National Library of Medicine and National Human Genome Research Institute (A.M.P. and S.K.) and the following extramural NIH grants: R01AI101112 (J.R.P.), R35GM118336 (R.S.M. and W.J.G.), R21AI121853 (M.V.S., I.V.S. and A.S.), R01AI123338 (Z.T.), T32GM007739 (M.H.), NIH/NCATS UL1TR000043 (Rockefeller University), DP2OD008540 (E.L.A.), U01AI088647, 1R01AI121211 (W.C.B. IV), Fogarty Training Grant D43TW001130-08, U01HL130010 (E.L.A.), UM1HG009375 (E.L.A), 5K22AI113060 (O.S.A.), 1R21AI123937 (O.S.A.), and R00DC012069 (C.S.M.), Defence Advanced Research Project Agency: HR0011-17-2- 0047 (O.S.A.). Other support was provided by Jane Coffin Childs Memorial Fund (B.J.M.), Center for Theoretical Biological Physics postdoctoral fellowship (O.D.), Robertson Foundation (L.Z.), and McNair & Welch (Q-1866) Foundations (E.L.A.), French Government’s Investissement d’Avenir program, Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID to L.L.), Agence Nationale de la Recherche grant ANR-17-ERC2-0016-01 (L.L.), European Union’s Horizon 2020 research and innovation program under ZikaPLAN grant agreement no. 734584 (L.L.), Pew and Searle Scholars Programs (C.S.M.), Klingenstein-Simons Fellowship in the Neurosciences (C.S.M.). A.M.W., B.J.W., J.E.C. and S.N.M. were supported by Verily Life Sciences. L.B.V. is an investigator of the Howard Hughes Medical Institute., We thank R. Andino, S. Emrich and D. Lawson (Vectorbase), A. A. James, M. Kunitomi, C. Nusbaum, D. Severson, N. Whiteman, T. Dickinson, M. Hartley and B. Rice (Dovetail Genomics) for early participation in the AGWG, C. Bargmann, D. Botstein, E. Jarvis and E. Lander for encouragement and facilitation. N. Keivanfar, D. Jaffe and D. M. Church (10X Genomics) prepared DNA for structural-variant analysis. We thank A. Harmon of the New York Times and acknowledge generous pro bono data and analysis from our corporate collaborators, ANR-17-ERC2-0016,GxG,Base génétique de la spécificité génotype-génotype dans l'interaction naturelle entre un virus et son insecte vecteur(2017), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: no. 734584, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), University of California [Riverside] (UCR), University of California, Biochemistry, Entomology, Fralin Life Sciences Institute, Howard Hughes Medical Institute (HHMI)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), The Rockefeller University [New-York], Howard Hughes Medical Institute [Berkeley], University of California [Berkeley], Baylor College of Medicine ( BCM ), Baylor College of Medicine, National Human Genome Research Institute ( NHGRI ), California Institute of Technology ( CALTECH ), Broad Institute of MIT and Harvard ( BROAD INSTITUTE ), Harvard Medical School [Boston] ( HMS ) -Massachusetts General Hospital [Boston] ( MGH ) -Massachusetts Institute of Technology ( MIT ), Liverpool John Moore University ( ljmu ), University College of London [London] ( UCL ), Colorado State University [Fort Collins] ( CSU ), National Center for Biotechnology Information ( NCBI ), Armed Forces Research Institute of Medical Sciences [Bangkok] ( AFRIMS ), Vecteurs - Infections tropicales et méditerranéennes ( VITROME ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut de Recherche Biomédicale des Armées ( IRBA ), Interactions Virus-Insectes - Insect-Virus Interactions ( IVI ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche Biomédicale des Armées [Antenne Marseille] ( IRBA ), University of California [Riverside] ( UCR ), Liverpool School of Tropical Medicine ( LSTM ), University of California [San Diego] ( UC San Diego ), University of Illinois at Urbana-Champaign [Urbana]
Jazyk: angličtina
Rok vydání: 2018
Předmět:
0301 basic medicine
Male
and promotion of well-being
[SDV]Life Sciences [q-bio]
Genome
Insect
Dengue virus
medicine.disease_cause
Dengue fever
Insecticide Resistance
Aedes
Pyrethrins
Chikungunya
Glutathione Transferase
Genetics
education.field_of_study
Multidisciplinary
Genome
biology
Yellow fever
Genomics
Reference Standards
3. Good health
[ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Infectious Diseases
Multigene Family
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Female
Infection
Biotechnology
DNA Copy Number Variations
General Science & Technology
1.1 Normal biological development and functioning
Population
Aedes aegypti
Mosquito Vectors
Arbovirus Infections
Arbovirus
Insect Control
Article
Vaccine Related
03 medical and health sciences
QH301
Rare Diseases
Underpinning research
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
medicine
Animals
education
QR355
3.2 Interventions to alter physical and biological environmental risks
[SDV.GEN]Life Sciences [q-bio]/Genetics
Prevention
Human Genome
Genetic Variation
Molecular Sequence Annotation
Dengue Virus
Sex Determination Processes
medicine.disease
biology.organism_classification
Prevention of disease and conditions
Vector-Borne Diseases
030104 developmental biology
Emerging Infectious Diseases
Good Health and Well Being
Genetics
Population
Vector (epidemiology)
Insect
Arboviruses
[SDV.EE.IEO]Life Sciences [q-bio]/Ecology
environment/Symbiosis
Zdroj: NATURE
Nature
Nature, 2018, 563 (7732), pp.501-507. ⟨10.1038/s41586-018-0692-z⟩
Nature, vol 563, iss 7732
Nature, Nature Publishing Group, 2018, 563 (7732), pp.501-507. ⟨10.1038/s41586-018-0692-z⟩
Nature, Nature Publishing Group, 2018, 563 (7732), pp.501-507. 〈10.1038/s41586-018-0692-z〉
ISSN: 0028-0836
1476-4687
1476-4679
DOI: 10.1038/s41586-018-0692-z⟩
Popis: Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector. National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [U19AI110818]; USDA [2017-05741]; NIH Intramural Research Program; National Library of Medicine; National Human Genome Research Institute; NSF [PHY-1427654]; NIH [R01AI101112, R35GM118336, R21AI121853, R01AI123338, T32GM007739, NIH/NCATS UL1TR000043, DP2OD008540, U01AI088647, 1R01AI121211, D43TW001130-08, U01HL130010, UM1HG009375, 5K22AI113060, 1R21AI123937, R00DC012069]; Defence Advanced Research Project Agency [HR0011-17-2-0047]; Jane Coffin Childs Memorial Fund; Center for Theoretical Biological Physics postdoctoral fellowship; Robertson Foundation; McNair Foundation; Welch Foundation [Q-1866]; French Government's Investissement d'Avenir program, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases [ANR-10-LABX-62-IBEID]; Agence Nationale de la Recherche [ANR-17-ERC2-0016-01]; European Union [734584]; Pew and Searle Scholars Programs; Klingenstein-Simons Fellowship in the Neurosciences; Verily Life Sciences We thank R. Andino; S. Emrich and D. Lawson (Vectorbase); A. A. James, M. Kunitomi, C. Nusbaum, D. Severson, N. Whiteman; T. Dickinson, M. Hartley and B. Rice (Dovetail Genomics) for early participation in the AGWG; C. Bargmann, D. Botstein, E. Jarvis and E. Lander for encouragement and facilitation. N. Keivanfar, D. Jaffe and D. M. Church (10X Genomics) prepared DNA for structural-variant analysis. We thank A. Harmon of the New York Times and acknowledge generous pro bono data and analysis from our corporate collaborators. This research was supported in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under grant number U19AI110818 to the Broad Institute (S.N.R. and D.E.N.); USDA 2017-05741 (E.L.A.); NSF PHY-1427654 Center for Theoretical Biological Physics (E.L.A.); NIH Intramural Research Program, National Library of Medicine and National Human Genome Research Institute (A.M.P. and S.K.) and the following extramural NIH grants: R01AI101112 (J.R.P.), R35GM118336 (R.S.M. and W.J.G.), R21AI121853 (M.V.S., I.V.S. and A. S.), R01AI123338 (Z.T.), T32GM007739 (M.H.), NIH/NCATS UL1TR000043 (Rockefeller University), DP2OD008540 (E.L.A.), U01AI088647, 1R01AI121211 (W.C.B. IV), Fogarty Training Grant D43TW001130-08, U01HL130010 (E.L.A.), UM1HG009375 (E.L.A), 5K22AI113060 (O.S.A.), 1R21AI123937 (O.S.A.), and R00DC012069 (C.S.M.); Defence Advanced Research Project Agency: HR0011-17-2-0047 (O.S.A.). Other support was provided by Jane Coffin Childs Memorial Fund (B.J.M.), Center for Theoretical Biological Physics postdoctoral fellowship (O.D.), Robertson Foundation (L.Z.), and McNair & Welch (Q-1866) Foundations (E.L.A.), French Government's Investissement d'Avenir program, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID to L.L.), Agence Nationale de la Recherche grant ANR-17-ERC2-0016-01 (L.L.), European Union's Horizon 2020 research and innovation program under ZikaPLAN grant agreement no. 734584 (L.L.), Pew and Searle Scholars Programs (C.S.M.), Klingenstein-Simons Fellowship in the Neurosciences (C.S.M.). A.M.W., B.J.W., J.E.C. and S.N.M. were supported by Verily Life Sciences. L.B.V. is an investigator of the Howard Hughes Medical Institute.
Databáze: OpenAIRE
Externí odkaz: