Genome Biology (Aug 2020)
Improved reference genome of the arboviral vector Aedes albopictus
- Umberto Palatini,
- Reem A. Masri,
- Luciano V. Cosme,
- Sergey Koren,
- Françoise Thibaud-Nissen,
- James K. Biedler,
- Flavia Krsticevic,
- J. Spencer Johnston,
- Rebecca Halbach,
- Jacob E. Crawford,
- Igor Antoshechkin,
- Anna-Bella Failloux,
- Elisa Pischedda,
- Michele Marconcini,
- Jay Ghurye,
- Arang Rhie,
- Atashi Sharma,
- Dmitry A. Karagodin,
- Jeremy Jenrette,
- Stephanie Gamez,
- Pascal Miesen,
- Patrick Masterson,
- Adalgisa Caccone,
- Maria V. Sharakhova,
- Zhijian Tu,
- Philippos A. Papathanos,
- Ronald P. Van Rij,
- Omar S. Akbari,
- Jeffrey Powell,
- Adam M. Phillippy,
- Mariangela Bonizzoni
Affiliations
- Umberto Palatini
- Department of Biology and Biotechnology, University of Pavia
- Reem A. Masri
- Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University
- Luciano V. Cosme
- Department of Ecology and Evolutionary Biology, Yale University
- Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
- Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- James K. Biedler
- Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University
- Flavia Krsticevic
- Department of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem
- J. Spencer Johnston
- Department of Entomology, Texas A&M University
- Rebecca Halbach
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences
- Jacob E. Crawford
- Verily Life Sciences
- Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology
- Anna-Bella Failloux
- Department of Virology, Arbovirus and Insect Vectors Units, Institut Pasteur
- Elisa Pischedda
- Department of Biology and Biotechnology, University of Pavia
- Michele Marconcini
- Department of Biology and Biotechnology, University of Pavia
- Jay Ghurye
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
- Atashi Sharma
- Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University
- Dmitry A. Karagodin
- Laboratory of Evolutionary Genomics of Insects, The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences
- Jeremy Jenrette
- Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University
- Stephanie Gamez
- Division of Biological Sciences, University of California, San Diego
- Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences
- Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University
- Maria V. Sharakhova
- Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University
- Zhijian Tu
- Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University
- Philippos A. Papathanos
- Department of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem
- Ronald P. Van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences
- Omar S. Akbari
- Division of Biological Sciences, University of California, San Diego
- Jeffrey Powell
- Department of Ecology and Evolutionary Biology, Yale University
- Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
- Mariangela Bonizzoni
- Department of Biology and Biotechnology, University of Pavia
- DOI
- https://doi.org/10.1186/s13059-020-02141-w
- Journal volume & issue
-
Vol. 21,
no. 1
pp. 1 – 29
Abstract
Abstract Background The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.
Keywords
