Draft genome sequence of scale drop disease virus (SDDV) retrieved from metagenomic investigation of infected barramundi,Lates calcarifer (Bloch, 1790) |
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| Authors: | Pattanapon Kayansamruaj Chayanit Soontara Ha T Dong Kornsunee Phiwsaiya Saengchan Senapin |
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| Institution: | 1. Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand;2. Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, Thailand;3. Faculty of Science, Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand;4. Faculty of Science, Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand |
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| Abstract: | Scale drop disease virus (SDDV) is a novel viral pathogen considered to be distributed in farmed barramundi (Lates calcarifer) in South-East Asia. Despite the severity of the disease, only limited genomic information related to SDDV is available. In this study, samples of SDDV-infected fish collected in 2019 were used. The microbiome of brain tissue was investigated using Illumina HiSeq DNA sequencing. Taxonomic analysis showed that SDDV was the main pathogen contained in the affected barramundi. De novo metagenome assembly recovered the SDDV genome, named isolate TH2019, 131 kb in length, and comprised of 135 ORFs. Comparison between this genome and the Singaporean SDDV reference genome revealed that the nucleotide identity within the aligned region was 99.97%. Missense, frameshift, insertion and deletion mutations were identified in 26 ORFs. Deletion of four deduced amino acid sequence in ORF_030L, identical to the SDDV isolate previously identified in Thailand, would be a potential biomarker for future strain classification. Interestingly, the genome of SDDV TH2019 harboured a unique 7,695-bp-long genomic region containing six hypothetical protein-encoded genes. Collectively, this study demonstrated that the SDDV genome can be sequenced directly, although with limited coverage depth, using metagenomic analysis of barramundi sample with severe infection. |
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| Keywords: | genome Lates calcarifer metagenomics mutation scale drop disease virus |
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