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ARS Home » Southeast Area » Auburn, Alabama » Aquatic Animal Health Research » Research » Publications at this Location » Publication #404449
Research Project: Integrated Research to Improve Aquatic Animal Health in Warmwater Aquaculture

Location: Aquatic Animal Health Research

Title: Genome sequence of white spot syndrome virus (WSSV) isolated from Alabama crayfish

Author
item Abernathy, Jason
item BRUCE, TIMOTHY - Auburn University

Submitted to: Genbank
Publication Type: Database / Dataset
Publication Acceptance Date: 4/24/2023
Publication Date: 10/11/2023
Citation: Abernathy, J.W., Bruce, T.J. 2023. Genome sequence of white spot syndrome virus (WSSV) isolated from Alabama crayfish. Genbank.

Interpretive Summary:

Technical Abstract: White spot syndrome virus (WSSV) is a double stranded DNA virus that causes mass mortalities to both the shrimp and crayfish aquaculture industries worldwide. Here, we sequenced and characterized a WSSV isolate from infected crayfish harvested in the Southeastern United States for the first time. Total DNA from a heavily-infected red swamp crayfish (Procambarus clarkii) was isolated. DNA was assessed for quality and quantity and then the sample was processed for Oxford Nanopore Technologies (ONT) sequencing using the Ligation Sequencing Kit V14. The DNA library was loaded on a single flow-cell and sequencing was performed on the GridION Mk1. During the sequencing run, adaptive sampling was utilized, where the red swamp crayfish genome (Accession #GCA_020424385.2) was actively subtracted from the reads and only those sequences not matching the host genome were kept. Post sequencing, raw FAST5 files were basecalled using the Super Accurate configuration along with alignment to all WSSV genomes in GenBank to date (n=13). Resultant FASTQ files were analyzed using Flye, with the constraints of expecting an approximate 300 kb genome along with the nano-hq option for ONT high-quality reads. A genome assembly of WSSV was produced, with length of 285,974 bp and G/C content of 41.2%. Mean coverage of the genome was 43x, with an assembly N50 of 4,147. Annotation of the genome was accomplished via Glimmer3 and BLASTx to the nr database, revealing 199 genes with average length of 1,313 bp. The WSSV genome sequence and annotation have been submitted to the NCBI viral genomes database, and will be a valuable resource for study of this pathogen.