Improved reference genome of the arboviral vector Aedes albopictus
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RESEARCH
Open Access
Improved reference genome of the arboviral vector Aedes albopictus Umberto Palatini1†, Reem A. Masri2†, Luciano V. Cosme3, Sergey Koren4, Françoise Thibaud-Nissen5, James K. Biedler2, Flavia Krsticevic6, J. Spencer Johnston7, Rebecca Halbach8, Jacob E. Crawford9, Igor Antoshechkin10, Anna-Bella Failloux11, Elisa Pischedda1, Michele Marconcini1, Jay Ghurye4, Arang Rhie4, Atashi Sharma2, Dmitry A. Karagodin12, Jeremy Jenrette2, Stephanie Gamez14, Pascal Miesen8, Patrick Masterson5, Adalgisa Caccone3, Maria V. Sharakhova2,12,13, Zhijian Tu2, Philippos A. Papathanos6, Ronald P. Van Rij8, Omar S. Akbari14, Jeffrey Powell3†, Adam M. Phillippy4† and Mariangela Bonizzoni1*† * Correspondence: m.bonizzzoni@ unipv.it † Jeffrey Powell, Adam M. Phillippy, and Mariangela Bonizzoni jointly supervised this work. 1 Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy Full list of author information is available at the end of the article
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: Ae. albopictus, Genome, miRNAs, piRNA clusters, Viral integrations, Immunity, Sex locus, Population differentiation, Developmental transcriptome
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