Title

Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from host infected tissues, 2024

Date (Creation)

2021-03-01

Date (Publication)

2024-05-16

Citation identifier

FR-330-715-368-00032-IFR_BIOINFO_OSTREID_HERPESVIRUS_OSHV

Abstract

Raw data from 6 ONT runs performed to evaluate 7 DNA extraction kits on gills and mantle of moribund Pacific oysters using whole-sequencing or adaptive sampling to enrich for OsHV-1 sequences.

Credit

IFREMER, Unité Adaptation et Santé des Invertébrés Marins

Point of contact

Organisation name	Individual name	Electronic mail address	Role
IFREMER		sismer@ifremer.fr	Publisher
IFREMER	Dotto-Maurel Aurélie	adottoma@ifremer.fr	Author
IFREMER	Pelletier Camille	camille.pelletier@partenaire-extrerieur.ifremer.fr	Author
IFREMER	Degremont Lionel	Lionel.Degremont@ifremer.fr	Author
IFREMER	Heurtebise Serge	Serge.Heurtebise@ifremer.fr	Author
IFREMER	Morga Benjamin	Benjamin.Morga@ifremer.fr	Author
IFREMER	Chevignon Germain	Germain.Chevignon@ifremer.fr	Author

GEMET - INSPIRE themes, version 1.0

• Habitats et biotopes

Thèmes Sextant

• /Milieu biologique/Bio-Informatique

ODATIS aggregation parameters and Essential Variable names

• Bioinformatique

Use limitation

CC-BY (Creative Commons - Attribution)

Access constraints

License

Use constraints

License

Language

Français

Character set

UTF8

Reference system identifier

EPSG / WGS 84 (EPSG:4326) / 8.6

Distribution format

Name	Version

OnLine resource

Protocol	Linkage	Name
NETWORK:LINK	/home/ref-bioinfo-public/ifremer/asim/2023_WGS_oshv1_7_kits
WWW:DOWNLOAD	https://data-dataref.ifremer.fr/bioinfo/ifremer/asim/2023_WGS_oshv1_7_kits/	Lien de téléchargement (https)
WWW:LINK	https://www.ebi.ac.uk/ena/browser/view/PRJEB82928	Publication ENA

OnLine resource

Protocol	Linkage	Name
DOI	https://doi.org/10.12770/1a301465-aee7-42c2-a950-7708f422a6aa	Digital Object Identifier (DOI)

Hierarchy level

Dataset

Statement

Since the 1990s, the Pacific oyster Magallana gigas has faced significant mortality due to the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole genome analysis. Identification of the best method for extraction of high molecular weight (HMW) DNA and development of accurate bioinformatic pipelines for its characterization are now required. To this end, we evaluated and compared six HWM and one conventional DNA extraction kit for their ability to extract OsHV-1 DNA from M. gigas-infected tissues. We then evaluated the ability of ONT sequencing to produce an accurate OsHV-1 genome from both whole genome and “adaptive sampling” (AS) sequencing approaches. Finally, we evaluated the efficiency of bioinformatics tools for de novo assembly and consensus calling to generate accurate OsHV-1 genomes. The HMW DNA extraction kit coupled with ONT sequencing and dedicated bioinformatics tools allowed us to produce near perfect OsHV-1 genomes compared to those assembled using Illumina technology. The AS approach allowed up to 60% enrichment for viral data, and the long reads generated by ONT allowed the characterization of OsHV-1 isomers. Together with its portability, this sequencing shows great promise as a diagnostic tool for the characterization of unculturable aquatic viruses directly from host tissues.

Metadata

File identifier

1a301465-aee7-42c2-a950-7708f422a6aa

Metadata language

Français

Character set

UTF8

Hierarchy level

Dataset

Date stamp

2024-12-17T13:35:02.213566Z

Metadata standard name

ISO 19115:2003/19139 - SEXTANT

Metadata standard version

1.0

Metadata author

Organisation name	Individual name	Electronic mail address	Role
IFREMER	Dotto-Maurel Aurélie	adottoma@ifremer.fr	Local service desk