Improved reference genome of the arboviral vector Aedes albopictus
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...
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| Language: | English |
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BMC
2020-08-01
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| Series: | Genome Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02141-w |
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| author | 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 |
| author_facet | 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 |
| author_sort | Umberto Palatini |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T13:45:32Z |
| format | Article |
| id | doaj.art-1e26c972bac24388a3d71c9152213795 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-13T13:45:32Z |
| publishDate | 2020-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-1e26c972bac24388a3d71c91522137952022-12-21T23:43:25ZengBMCGenome Biology1474-760X2020-08-0121112910.1186/s13059-020-02141-wImproved reference genome of the arboviral vector Aedes albopictusUmberto Palatini0Reem A. Masri1Luciano V. Cosme2Sergey Koren3Françoise Thibaud-Nissen4James K. Biedler5Flavia Krsticevic6J. Spencer Johnston7Rebecca Halbach8Jacob E. Crawford9Igor Antoshechkin10Anna-Bella Failloux11Elisa Pischedda12Michele Marconcini13Jay Ghurye14Arang Rhie15Atashi Sharma16Dmitry A. Karagodin17Jeremy Jenrette18Stephanie Gamez19Pascal Miesen20Patrick Masterson21Adalgisa Caccone22Maria V. Sharakhova23Zhijian Tu24Philippos A. Papathanos25Ronald P. Van Rij26Omar S. Akbari27Jeffrey Powell28Adam M. Phillippy29Mariangela Bonizzoni30Department of Biology and Biotechnology, University of PaviaDepartment of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State UniversityDepartment of Ecology and Evolutionary Biology, Yale UniversityGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthDepartment of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State UniversityDepartment of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemDepartment of Entomology, Texas A&M UniversityDepartment of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life SciencesVerily Life SciencesDivision of Biology and Biological Engineering, California Institute of TechnologyDepartment of Virology, Arbovirus and Insect Vectors Units, Institut PasteurDepartment of Biology and Biotechnology, University of PaviaDepartment of Biology and Biotechnology, University of PaviaGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of HealthGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of HealthDepartment of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State UniversityLaboratory of Evolutionary Genomics of Insects, The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of SciencesDepartment of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State UniversityDivision of Biological Sciences, University of California, San DiegoDepartment of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life SciencesNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthDepartment of Ecology and Evolutionary Biology, Yale UniversityDepartment of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State UniversityDepartment of Entomology and the Fralin Life Science Institute, Virginia Polytechnic and State UniversityDepartment of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemDepartment of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life SciencesDivision of Biological Sciences, University of California, San DiegoDepartment of Ecology and Evolutionary Biology, Yale UniversityGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of HealthDepartment of Biology and Biotechnology, University of PaviaAbstract 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.http://link.springer.com/article/10.1186/s13059-020-02141-wAe. albopictusGenomemiRNAspiRNA clustersViral integrationsImmunity |
| spellingShingle | 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 Improved reference genome of the arboviral vector Aedes albopictus Genome Biology Ae. albopictus Genome miRNAs piRNA clusters Viral integrations Immunity |
| title | Improved reference genome of the arboviral vector Aedes albopictus |
| title_full | Improved reference genome of the arboviral vector Aedes albopictus |
| title_fullStr | Improved reference genome of the arboviral vector Aedes albopictus |
| title_full_unstemmed | Improved reference genome of the arboviral vector Aedes albopictus |
| title_short | Improved reference genome of the arboviral vector Aedes albopictus |
| title_sort | improved reference genome of the arboviral vector aedes albopictus |
| topic | Ae. albopictus Genome miRNAs piRNA clusters Viral integrations Immunity |
| url | http://link.springer.com/article/10.1186/s13059-020-02141-w |
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