Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections
| Autor: | Ewa Borzym, Saliha Hammoumi, Jean-Christophe Avarre, Philippe Leleux, Tatiana Vallaeys, Ayi Santika, Christophe Klopp |
|---|---|
| Přispěvatelé: | Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université de Montpellier (UM), Main Center for Freshwater Aquaculture Development, Partenaires INRAE, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Plateforme Bio-Informatique - Génotoul, National Veterinary Research Institute, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS) |
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
Veterinary Medicine
0301 basic medicine Cyprinid herpesvirus 3 ved/biology.organism_classification_rank.species Genome Targeted genomic enrichment Mixed infection Variability KOI HERPESVIRUS KHV NEIGHBOR-JOINING METHOD PROKARYOTIC GENOMES COMMON CARP GENERATION ALIGNMENT REPEATS ISOLATE SCALE lcsh:Medicine Marine Biology General Biochemistry Genetics and Molecular Biology Deep sequencing Nucleotide diversity 03 medical and health sciences Common carp [INFO]Computer Science [cs] [MATH]Mathematics [math] Carp Genetics biology ved/biology General Neuroscience lcsh:R 04 agricultural and veterinary sciences General Medicine biology.organism_classification genomic DNA 030104 developmental biology GenBank Aquaculture Fisheries and Fish Science 040102 fisheries 0401 agriculture forestry and fisheries General Agricultural and Biological Sciences |
| Zdroj: | PeerJ PeerJ, PeerJ, 2016, 4, ⟨10.7717/peerj.2516⟩ PeerJ, 2016, 4, ⟨10.7717/peerj.2516⟩ PeerJ, Vol 4, p e2516 (2016) Europe PubMed Central PeerJ (4), . (2016) |
| ISSN: | 2167-8359 |
| DOI: | 10.7717/peerj.2516⟩ |
| Popis: | Koi herpesvirus disease (KHVD) is an emerging disease that causes mass mortality in koi and common carp,Cyprinus carpioL. Its causative agent is Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV). Although data on the pathogenesis of this deadly virus is relatively abundant in the literature, still little is known about its genomic diversity and about the molecular mechanisms that lead to such a high virulence. In this context, we developed a new strategy for sequencing full-length CyHV-3 genomes directly from infected fish tissues. Total genomic DNA extracted from carp gill tissue was specifically enriched with CyHV-3 sequences through hybridization to a set of nearly 2 million overlapping probes designed to cover the entire genome length, using KHV-J sequence (GenBank accession numberAP008984) as reference. Applied to 7 CyHV-3 specimens from Poland and Indonesia, this targeted genomic enrichment enabled recovery of the full genomes with >99.9% reference coverage. The enrichment rate was directly correlated to the estimated number of viral copies contained in the DNA extracts used for library preparation, which varied between ∼5000 and ∼2×107. The average sequencing depth was >200 for all samples, thus allowing the search for variants with high confidence. Sequence analyses highlighted a significant proportion of intra-specimen sequence heterogeneity, suggesting the presence of mixed infections in all investigated fish. They also showed that inter-specimen genetic diversity at the genome scale was very low (>99.95% of sequence identity). By enabling full genome comparisons directly from infected fish tissues, this new method will be valuable to trace outbreaks rapidly and at a reasonable cost, and in turn to understand the transmission routes of CyHV-3. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|