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1. Improved reference genome of the arboviral vector Aedes albopictus

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, and Mariangela Bonizzoni

Subjects
Ae. albopictus, Genome, miRNAs, piRNA clusters, Viral integrations, Immunity, Biology (General), QH301-705.5, Genetics, QH426-470
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.

Published
2020
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2. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

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, and Mariangela Bonizzoni

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Published
2021
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5. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

Author

Pascal Miesen, Rebecca Halbach, Omar S. Akbari, Philippos Aris Papathanos, Elisa Pischedda, Ronald P. van Rij, Flavia Krsticevic, Françoise Thibaud-Nissen, Atashi Sharma, Arang Rhie, Luciano V. Cosme, Michele Marconcini, Zhijian Tu, Anna-Bella Failloux, Jeffrey R. Powell, Maria V. Sharakhova, James K. Biedler, Jacob E. Crawford, Reem A. Masri, Sergey Koren, D. A. Karagodin, Igor Antoshechkin, Jeremy Jenrette, Stephanie Gamez, Adam M. Phillippy, Umberto Palatini, Adalgisa Caccone, Mariangela Bonizzoni, J. Spencer Johnston, Patrick Masterson, Jay Ghurye, Università degli Studi di Pavia, Virginia Polytechnic Institute and State University [Blacksburg], Yale University [New Haven], National Human Genome Research Institute (NHGRI), National Center for Biotechnology Information (NCBI), The Hebrew University of Jerusalem (HUJ), Texas A&M University [College Station], Radboud Institute for Molecular Life Sciences [Nijmegen, the Netherlands], Verily Life Sciences Inc, California Institute of Technology (CALTECH), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris], Siberian Branch of the Russian Academy of Sciences (SB RAS), University of California [San Diego] (UC San Diego), University of California, Tomsk State University [Tomsk], Università degli Studi di Pavia = University of Pavia (UNIPV), Institut Pasteur [Paris] (IP), and University of California (UC)

Subjects
Aedes albopictus, QH301-705.5, [SDV]Life Sciences [q-bio], Computational biology, Mosquito Vectors, Biology, QH426-470, Chromosomes, 03 medical and health sciences, 0302 clinical medicine, Genome Size, Aedes, Genetics, Animals, RNA, Small Interfering, Biology (General), Author Correction, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Genome, Immunity, Chromosome Mapping, biology.organism_classification, Human genetics, 3. Good health, Insect Vectors, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Vector (epidemiology), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Transcriptome, 030217 neurology & neurosurgery, Arboviruses, Reference genome
Abstract

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.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.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.

Published
2021
Full Text
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6. Improved reference genome of the arboviral vector Aedes albopictus

Author

Pascal Miesen, Atashi Sharma, Michele Marconcini, Zhijian Tu, Philippos Aris Papathanos, Umberto Palatini, Jim Biedler, D. A. Karagodin, Omar S. Akbari, Françoise Thibaud-Nissen, Stephanie Gamez, Mariangela Bonizzoni, Jacob E. Crawford, Anna-Bella Failloux, Elisa Pischedda, R. P. van Rij, Sergey Koren, Luciano V. Cosme, Adam M. Phillippy, Jeremy Jenrette, Jeffrey R. Powell, Flavia Krsticevic, Rebecca Halbach, Reem A. Masri, J.S. Johnston, Jay Ghurye, Igor Antoshechkin, Adalgisa Caccone, Arang Rhie, and Maria V. Sharakhova

Subjects
0303 health sciences, Aedes albopictus, viruses, fungi, Sequence assembly, Piwi-interacting RNA, Locus (genetics), Biology, biology.organism_classification, Genome, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, Expression data, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, Reference genome
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.

Published
2020

7. Improved reference genome of the arboviral vector Aedes albopictus

Author

J. Spencer Johnston, Pascal Miesen, Maria V. Sharakhova, Omar S. Akbari, D. A. Karagodin, Patrick Masterson, Jay Ghurye, Luciano V. Cosme, Umberto Palatini, Adam M. Phillippy, Anna-Bella Failloux, Ronald P. van Rij, James K. Biedler, Arang Rhie, Igor Antoshechkin, Mariangela Bonizzoni, Jacob E. Crawford, Sergey Koren, Jeremy Jenrette, Adalgisa Caccone, Reem A. Masri, Michele Marconcini, Zhijian Tu, Jeffrey R. Powell, Atashi Sharma, Rebecca Halbach, Stephanie Gamez, Elisa Pischedda, Flavia Krsticevic, Françoise Thibaud-Nissen, Philippos Aris Papathanos, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), Virginia Polytechnic Institute and State University [Blacksburg], Department of Ecology and Evolutionary Biology [New Haven], Yale University [New Haven], National Human Genome Research Institute (NHGRI), National Center for Biotechnology Information (NCBI), The Hebrew University of Jerusalem (HUJ), Texas A&M University [College Station], Radboud University Medical Center [Nijmegen], Verily Life Sciences Inc, California Institute of Technology (CALTECH), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Siberian Branch of the Russian Academy of Sciences (SB RAS), University of California [San Diego] (UC San Diego), University of California (UC), Tomsk State University [Tomsk], National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, 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., We would like to thank Francesca Scolari and Patrizia Chiari for the mosquito maintenance., European Project: 682394,H2020,ERC-2015-CoG,NIRV_HOST_INT(2016), European Project: 615680,EC:FP7:ERC,ERC-2013-CoG,VIVARNASILENCING(2014), Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, University of Pavia, University of Pavia, Institut Pasteur [Paris], and University of California

Subjects
lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Sequence assembly, Viral integrations, Genome, 0302 clinical medicine, Genome Size, Aedes, Population differentiation, lcsh:QH301-705.5, 0303 health sciences, Chromosome Mapping, Biological Sciences, 3. Good health, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, miRNAs, Infection, Sex locus, Biotechnology, Aedes albopictus, lcsh:QH426-470, albopictus, Bioinformatics, Developmental transcriptome, 1.1 Normal biological development and functioning, Ae, Locus (genetics), Mosquito Vectors, Computational biology, Biology, Small Interfering, Chromosomes, DNA sequencing, Vaccine Related, 03 medical and health sciences, Rare Diseases, All institutes and research themes of the Radboud University Medical Center, Underpinning research, Biodefense, Information and Computing Sciences, Genetics, Animals, Ae. albopictus, Gene, 030304 developmental biology, Prevention, Research, Human Genome, fungi, Immunity, biology.organism_classification, Human genetics, Insect Vectors, Vector-Borne Diseases, lcsh:Genetics, Emerging Infectious Diseases, Good Health and Well Being, lcsh:Biology (General), RNA, Generic health relevance, Transcriptome, Arboviruses, Environmental Sciences, piRNA clusters, 030217 neurology & neurosurgery, Reference genome
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.

Published
2020
Full Text
View/download PDF

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