Improved reference genome of the arboviral vector Aedes albopictus

Genome Biology

Umberto Palatini¹  Michele Marconcini¹  Mariangela Bonizzoni¹  Elisa Pischedda¹  Jeffrey Powell²  Luciano V. Cosme²  Adalgisa Caccone²  Jeremy Jenrette³  Atashi Sharma³  Reem A. Masri³  James K. Biedler³  Zhijian Tu³  Maria V. Sharakhova⁴  Flavia Krsticevic⁵  Philippos A. Papathanos⁵  J. Spencer Johnston⁶  Pascal Miesen⁷  Rebecca Halbach⁷  Ronald P. Van Rij⁷  Anna-Bella Failloux⁸  Stephanie Gamez⁹  Omar S. Akbari⁹  Igor Antoshechkin^1,10  Jay Ghurye^1,11  Adam M. Phillippy^1,11  Sergey Koren^1,11  Arang Rhie^1,11  Dmitry A. Karagodin^1,12  Françoise Thibaud-Nissen^1,13  Patrick Masterson^1,13  Jacob E. Crawford^1,14 

[1] Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy;Department of Ecology and Evolutionary Biology, Yale University, 06511-8934, New Haven, CT, USA;Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University, 24061, Blacksburg, VA, USA;Department of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State University, 24061, Blacksburg, VA, USA;Laboratory of Evolutionary Genomics of Insects, The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia;Laboratory of Ecology, Genetics and Environment Protection, Tomsk State University, 634041, Tomsk, Russia;Department of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel;Department of Entomology, Texas A&M University, 77843, College Station, TX, USA;Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands;Department of Virology, Arbovirus and Insect Vectors Units, Institut Pasteur, 75015, Paris, France;Division of Biological Sciences, University of California, San Diego, 92093-0349, La Jolla, CA, USA;Division of Biology and Biological Engineering, California Institute of Technology, 91125, Pasadena, CA, USA;Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 20892-2152, Bethesda, MD, USA;Laboratory of Evolutionary Genomics of Insects, The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia;National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, MD, USA;Verily Life Sciences, 94080, South San Francisco, CA, USA;

关键词: Ae. albopictus;    Genome;    miRNAs;    piRNA clusters;    Viral integrations;    Immunity;    Sex locus;    Population differentiation;    Developmental transcriptome;   

DOI  :  10.1186/s13059-020-02141-w

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionThe 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.

【 授权许可】

CC BY