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      Improved reference genome of Aedes aegypti informs arbovirus vector control

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          Abstract

          Female Aedes aegypti mosquitoes infect >400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding mosquito biology and developing tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the dramatically 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 elusive sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes important for insecticide resistance. Using high-resolution quantitative trait locus (QTL) 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.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Is Open Access

            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              Fast gapped-read alignment with Bowtie 2.

              As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                6 October 2018
                14 November 2018
                November 2018
                14 May 2019
                : 563
                : 7732
                : 501-507
                Affiliations
                [1 ]Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA.
                [2 ]Howard Hughes Medical Institute, New York, New York, USA.
                [3 ]Kavli Neural Systems Institute, New York, New York, USA.
                [4 ]The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
                [5 ]Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
                [6 ]Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
                [7 ]Center for Theoretical and Biological Physics, Rice University, Houston, Texas, USA.
                [8 ]Pacific Biosciences, Menlo Park, California, USA.
                [9 ]National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
                [10 ]Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.
                [11 ]Verily Life Sciences, South San Francisco, California, USA.
                [12 ]Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
                [13 ]Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
                [14 ]Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
                [15 ]Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.
                [16 ]Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
                [17 ]Liverpool John Moores University, Liverpool, United Kingdom.
                [18 ]Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China.
                [19 ]Department of Biochemistry, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
                [20 ]Department of Entomology, Purdue University, West Lafayette, Indiana, USA.
                [21 ]Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
                [22 ]Centre for Respiratory Biology, UCL Respiratory, University College London, London, United Kingdom.
                [23 ]Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
                [24 ]Bionano Genomics, San Diego, California, USA.
                [25 ]National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
                [26 ]Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
                [27 ]Vector Biology and Control Section, Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand.
                [28 ]Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
                [29 ]Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
                [30 ]Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.
                [31 ]Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France.
                [32 ]Aix Marseille Université, IRD, AP-HM, SSA, UMR Vecteurs – Infections Tropicales et Méditerranéennes (VITROME), IHU - Méditerranée Infection, Marseille, France
                [33 ]The Connecticut Agricultural Experiment Station, New Haven, CT 06504 USA
                [34 ]Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.
                [35 ]Department of Entomology, University of California Riverside, Riverside, California, USA.
                [36 ]Department of Bioengineering, Rice University, Houston, Texas, USA.
                [37 ]Department of Pediatrics, Texas Children’s Hospital, Houston, Texas, USA.
                [38 ]Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, California, USA.
                [39 ]Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
                [40 ]Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
                [41 ]Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA.
                [42 ]Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, California, USA
                [43 ]Department of Entomology, Texas A&M University, College Station, Texas, USA.
                [44 ]Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia.
                [45 ]Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, New York, USA.
                [46 ]Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
                [47 ]Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
                Author notes
                [*]

                These authors contributed equally to this work.

                Correspondence to B.J.M: bnmtthws@ 123456gmail.com

                Author Contributions B.J.M. and L.B.V. conceived the study, coordinated data collection and analysis, designed the figures, and wrote the paper with input from all authors. B.J.M. developed and distributed animals and/or DNA of the LVP_AGWG strain. Pacific Biosciences sample preparation and sequencing: (P.P., M.L.S., J.M.); Assembly: (S.B.K., R.H., J.K., S.K., A.M.P.); Bionano optical mapping: (A.R.H., S.C., J.L., H.C.); Hi-C sample preparation, scaffolding, and deduplication: (O.D., S.S.B. A.D.O., A.P.A., E.L.A); Fig. 1c (B.R.E., A.G.-S., J.R.P); Fig. 1d (J.S.J.); Fig. 1f (L.Z.); Fig. 1g (E.C., V.S.J., V.K.K., M.R.M., T.D.M., B.J.M.); Fig. 1h (I.A., O.S.A., J.E.C., A.M.W. B.J.W., R.G.G.K., S.N.M., B.J.M).; Fig. 2 (C.S.M., H.M.R., Z.Z., N.H.R., B.J.M.); Fig. 3a-d (Z.T., M.V.S., I.V.S., A.S., Y.W., J.T., A.C.D., A.R.H., B.J.M.); Fig. 4 (G.D.W., B.J.M., A.R.H., S.B.K., A.M.P., S.K.); Fig. 5a-d (A.F., I.F., T.F., G.R., L.L.); Fig. 5e-g (C.L.C, K.S.-R., W.C.B.IV, B.J.M.); Extended Data Fig. 1a (B.J.M.); Extended Data Fig. 1b (J.S.J.); Extended Data Fig. 1c-d (O.D., S.S.B. A.D.O., A.P.A., E.L.A); Extended Data Fig 1e (S.B.K., J.K., O.D., E.L.A., S.K., A.M.P., B.J.M.); Extended Data Fig. 2a (A.R.H., B.J.M.); Extended Data Fig. 2b (E.C., V.S.J., V.K.K., M.R.M., T.D.M., B.J.M.); Extended Data Fig. 2c-d (M.H., B.J.M.); Extended Data Fig. 2e (A.S., I.V.S., M.V.S.); Extended Data Fig. 2f (C.A.B.-S., S.S., C.A.H.); Extended Data Fig. 3 (C.S.M., H.M.R., Z.Z., N.H.R., B.J.M.) Extended Data Fig. 47 (C.S.M., H.M.R., Z.Z., N.H.R., B.J.M.); Extended Data Fig. 8a (S.N.R., D.E.N.); Extended Data Fig. 8b-c (W.J.G., R.S.M., O.D., E.L.A. B.J.M.); Extended Data Fig. 8d (W.J.G., R.S.M.); Extended Data Fig. 9a-b (J.E.C., A.M.W., B.J.W., R.G.G.K., S.N.M); Extended Data Fig 9c-d (B.R.E., A.G.-S., J.R.P); Extended Data Fig. 10a-b (A.F., I.F., T.F, G.R., L.L.); Extended Data Fig. 10c-d (G.J.L., A.K.J., V.R., S.D.B., F.A.P, D.B.S.); Supplementary Data 1 (A.R.H.); Supplementary Data 2–3 (L.Z.); Supplementary Data 4–9 (I.A., O.S.A., J.E.C., A.M.W. B.J.W., R.G.G.K., S.N.M., B.J.M.); Supplementary Data 10–11 (E.C., V.S.J., V.K.K., M.R.M., T.D.M); Supplementary Data 12 (A.S., I.V.S., M.V.S.); Supplementary Data 13 (S.R., A.S.R.); Supplementary Data 14–16 (C.A.B.-S., S.S., C.A.H.); Supplementary Data 17–20 (C.S.M., H.M.R., Z.Z., N.H.R., B.J.M.); Supplementary Data 21 (S.N.R., D.E.N.); Supplementary Data 22 (W.J.G., R.S.M.); Supplementary Data 23 (G.D.W., B.J.M.); Supplementary Data 24 (G.J.L., A.K.J., V.R., S.D.B., F.A.P, D.B.S.).

                Article
                NIHMS1509065
                10.1038/s41586-018-0692-z
                6421076
                30429615
                61acf592-0ade-4386-b671-cc477ca6c4d9

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