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Improved reference genome of the arboviral vector Aedes albopictus

Palatini, Umberto and Masri, R. A. and Cosme, L. V. and Koren, S. and Thibaud-Nissen, F. and Biedler, J. K. and Krsticevic, F. and Johnston, J. S. and Halbach, R. and Crawford, J. E. and Antoshechkin, Igor and Failloux, A. and Pischedda, E. and Marconcini, M. and Ghurye, J. and Rhie, A. and Sharma, A. and Karagodin, D. A. and Jenrette, J. and Gamez, S. and Miesen, P. and Caccone, A. and Sharakhova, M. V. and Tu, Z. and Papathanos, P. A. and Van Rij, R. P. and Akbari, O. S. and Powell, J. and Phillippy, A. M. and Bonizzoni, M. (2020) Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology, 21 . Art. No. 215. ISSN 1465-6906. PMCID PMC7448346. https://resolver.caltech.edu/CaltechAUTHORS:20200303-102539665

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1186/s13059-020-02141-wDOIArticle
https://doi.org/10.1101/2020.02.28.969527DOIDiscussion Paper
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7448346/PubMed CentralArticle
ORCID:
AuthorORCID
Palatini, Umberto0000-0002-2435-2655
Antoshechkin, Igor0000-0002-9934-3040
Papathanos, P. A.0000-0001-8508-4554
Bonizzoni, M.0000-0003-0568-8564
Additional Information:© 2020 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Received 26 April 2020; Accepted 07 August 2020; Published 26 August 2020. We would like to thank Francesca Scolari and Patrizia Chiari for the mosquito maintenance. Peer review information: Kevin Pang was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Review history: The review history is available as Additional file 12. The authors would like to thank the following for their financial support of research: European Research Council (ERC-CoG 682394 to M. Bonizzoni; ERC-CoG 615680 to R.P. van Rij); Italian Ministry of Education, University and Research (FARE-MIUR project R1623HZAH5 to M. Bonizzoni and Dipartimenti Eccellenza Program 2018–2022 to Department of Biology and Biotechnology “L. Spallanzani,” University of Pavia); Human Frontiers Science Foundation (Research Grant number RGP0007/2017) to M. Bonizzoni and R.P. van Rij; National Institutes of Health (R21AI135258 to M. Sharakova; 1R01AI151004-01 and 1DP2AI152071-01 to O.S. Akbari; R01AI32409 to A. Caccone); Defense Advanced Research Project Agency (DARPA) Safe Genes Program Grant (HR0011-17-2-0047) to O.S. Akbari; Netherlands Organization for Scientific Research (VICI grant number 016.VICI.170.090) to R.P. van Rij; Israeli Ministry of Science and Technology (3-16795 to P.A. Papathanos); Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health to J. Ghurye, A. Rhie, and A.M. Phillippy; Intramural Research Program of the National Library of Medicine, National Institutes of Health to F. Thibaud-Niessen; generous UCSD lab. startup funds to O.S. Akbari. Author Contributions: Conceptualization, resources, and whole-genome sequencing: M. Bonizzoni and J. Powell. Assembly and Hi-C data-based scaffolding: S. Koren, J. Ghurye, A. Rhie, and A.M. Phillippy. Whole-genome assembly quality control and analyses: U. Palatini, E. Pischedda, M. Bonizzoni, F. Krsticevic, and P.A. Papathanos. Physical mapping: R. A Masri, A. Sharma, D.A. Karagodin, J. Jenrette, and M. Sharakova. Cytofluorimetric-based genome size analyses: J.S. Johnston. Small RNA seq libraries and sequencing: M. Marconcini and A. Failloux. nrEVE annotation: U. Palatini and E. Pischedda. piRNA clusters and miRNA annotation: R. Halbach, P. Miesen, and R.P. Van Rij. Genome annotation: F. Thibaud-Nissen and P. Masterson. Immunity genes: F. Krsticevic and P.A. Papathanos. M locus: J.K. Biedler and Z. Tu. Population genomics: L.V. Cosme, J.E. Crawford, and A. Caccone. Developmental transcriptome: I. Antoshechkin, S. Gamez, and O.S. Akbari. Figures: U. Palatini, R.A. Masri, M.V. Sharakova, R. Halbach, P. Miesen, R.P. Van Rij, J. Biedler, Z. Tu, F. Krstivevic, P.A. Papathanos, L.V. Cosme, J.E. Crawford, A. Caccone, S. Gamez, and O.S. Akbari. Manuscript writing team: M. Bonizzoni, U. Palatini, J. Powell, P.A. Papathanos, M.V. Sharakova, R. Halbach, P. Miesen, R.P. Van Rij, J. Tu, A. Caccone, S. Gamez, and O.S. Akbari. The authors read and approved the final manuscript. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: J.E. Crawford is employed by the Verily Life Sciences LLC. S. Koren has received travel compensation to present at Pacific Biosciences meetings. All remaining authors declare no competing interests.
Funders:
Funding AgencyGrant Number
European Research Council (ERC)682394
European Research Council (ERC)615680
Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR)R1623HZAH5
University of Pavia2018-2022
Human Frontier Science ProgramRGP0007/2017
NIHR21AI135258
NIH1R01AI151004-01
NIH1DP2AI152071-01
NIHR01AI32409
Defense Advanced Research Project Agency (DARPA)HR0011-17-2-0047
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)016.VICI.170.090
Ministry of Science and Technology (Israel)3-16795
National Human Genome Research InstituteUNSPECIFIED
National Library of MedicineUNSPECIFIED
University of California, San DiegoUNSPECIFIED
Subject Keywords:Ae. Albopictus; Genome; miRNAs; piRNA clusters; Viral integrations; Immunity; Sex locus; Population differentiation; Developmental transcriptome
PubMed Central ID:PMC7448346
Record Number:CaltechAUTHORS:20200303-102539665
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200303-102539665
Official Citation:Palatini, U., Masri, R.A., Cosme, L.V. et al. Improved reference genome of the arboviral vector Aedes albopictus. Genome Biol 21, 215 (2020). https://doi.org/10.1186/s13059-020-02141-w
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101677
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:03 Mar 2020 18:40
Last Modified:09 Sep 2020 19:39

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