1. Uncovering the repertoire of endogenous flaviviral elements in Aedes mosquito genomes
- Author
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Maria-Carla Saleh, Yann Verdier, Laura B. Dickson, Hervé Blanc, Joëlle Vinh, Yasutsugu Suzuki, Louis Lambrechts, Lionel Frangeul, Virus et Interférence ARN - Viruses and RNA Interference, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Interactions Virus-Insectes (IVI), Spectrométrie de Masse Biologique et Protéomique (USR3149 / FRE2032) (SMBP), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the European Research Council (FP7/2013-2019 ERC CoG 615220 to M.-C.S.), the French Government’s Investissement d’Avenir Program, Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID to L.L. and M.-C.S.), the City of Paris Emergence(s) Program in Biomedical Research (to L.L.), the European Union’s Horizon 2020 Research and Innovation Program under ZikaPLAN grant agreement no. 734584 (to L.L.), and the Conseil Régional Ile de France (Sesame 2010 grant agreement 10022268 to J.V.). Y.S. is supported by Roux-Cantarini postdoctoral fellowships and Japan Society for the Promotion of Science postdoctoral fellowships for research abroad., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 615220,EC:FP7:ERC,ERC-2013-CoG,RNAIMMUNITY(2015), European Project: 734584,ZikaPLAN, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
- Subjects
mosquito-borne viruses ,Genome, Insect ,medicine.disease_cause ,Genome ,MESH: Flavivirus/genetics ,Mass Spectrometry ,Nucleotide diversity ,Aedes ,MESH: DNA, Viral/genetics ,MESH: Animals ,Chikungunya ,Spotlight ,MESH: High-Throughput Nucleotide Sequencing ,MESH: Evolution, Molecular ,Recombination, Genetic ,Genetics ,0303 health sciences ,education.field_of_study ,biology ,Phylogenetic tree ,030302 biochemistry & molecular biology ,High-Throughput Nucleotide Sequencing ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,RNA, Viral ,MESH: Recombination, Genetic ,MESH: RNA, Viral/genetics ,endogenous viral elements ,MESH: Virus Integration ,MESH: Computational Biology ,Virus Integration ,Population ,ancient flaviviral infections ,Deep sequencing ,DNA sequencing ,Evolution, Molecular ,MESH: RNA, Viral/analysis ,Viral Proteins ,03 medical and health sciences ,MESH: Viral Proteins/analysis ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,medicine ,Animals ,viral infectious diseases ,mosquito genome ,education ,030304 developmental biology ,MESH: Mass Spectrometry ,MESH: Aedes/virology ,Flavivirus ,MESH: Genome, Insect ,fungi ,Computational Biology ,biology.organism_classification ,Virology ,MESH: Aedes/genetics ,MESH: DNA, Viral/analysis ,Genetic Diversity and Evolution ,DNA, Viral - Abstract
Endogenous viral elements derived from non-retroviral RNA viruses were described in various animal genomes. Whether they have a biological function such as host immune protection against related viruses is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) inAedesmosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs fromAe. albopictusand one fromAe. aegypticell lines. However, in-depth characterization of EFVEs in wild-type mosquito populations and individualsin vivohas not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in severalAe. albopictusandAe. aegyptipopulations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of piRNA-like small RNAs in antisense orientation, targeting the EFVEs and their flanking regionsin vivo. The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations from different geographical regions. We bioinformatically predicted several new EFVEs from a VietnameseAe. albopictuspopulation and observed variation in the occurrence of those elements among mosquito populations. Phylogenetic analysis of anAe. aegyptiEFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. Together, this study revealed substantial structural and nucleotide diversity of flaviviral integrations inAedesgenomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs.ImportanceEndogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, we decided to thoroughly characterized them to lay the foundation of the potential use of these EVEs to manipulate the mosquito antiviral response. Here, we focused on EVEs related to theFlavivirusgenus, to which dengue and Zika viruses belong, inAedesmosquito individuals from geographically distinct areas. We showed the existencein vivoof flaviviral EVEs previously identified in mosquito cell lines and we detected new ones. We showed that EVEs have evolved differently in each mosquito population. They produced transcripts and small RNAs, but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs inAedesmosquito populations and suggests a role in the host antiviral system.
- Published
- 2017
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