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http://dx.doi.org/10.7847/jfp.2022.35.1.129

The complete genome sequence of a white spot syndrome virus isolated from Litopenaeus vannamei  

Lee, A-reum (School of Marine and Fisheries Life Science, Pukyong National University)
Kong, Kyoung-Hui (Department of Aqualife Medicine, Chonnam National University)
Kim, Hwi-Jin (Department of Aqualife Medicine, Chonnam National University)
Oh, Myung-Joo (Department of Aqualife Medicine, Chonnam National University)
Kim, Do-Hyung (Department of Aquatic life Medicine, Pukyong National University)
Kim, Jong-Oh (School of Marine and Fisheries Life Science, Pukyong National University)
Kim, Wi-Sik (Department of Aqualife Medicine, Chonnam National University)
Publication Information
Journal of fish pathology / v.35, no.1, 2022 , pp. 129-133 More about this Journal
Abstract
The full genome sequence of a Korean white spot syndrome virus (WSSV, isolate: WSSV-GoC18) is presented here. We obtained a total of 12,320,554 reads with 291,172 bases, 170 gene, and 170 coding DNA sequence, which were assembled in 1 contig. Phylogenetic analysis revealed that the WSSV-GoC18 was closely related to Chinese isolate (WSSV-PC) and distinctly different with previously reported a Korean isolate (WSSV K-LV1). The complete genome sequence of WSSV isolates will be of great help in molecular epidemiological studies, contributing to molecular diagnosis and disease prevention in shrimp aquaculture.
Keywords
white spot syndrome virus; WSSV; complete genome sequence;
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1 Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., Pyshkin, A.V., Sirotkin, A.V., Vyahhi, N., Tesler, G., Alekseyev, M.A. and Pevzner, P.A.: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19: 455-477. 2012.   DOI
2 Chai, C.Y., Yoon, J., Lee, Y.S., Kim, Y.B. and Choi, T.J.: Analysis of the complete nucleotide sequence of a white spot syndrome virus isolated from pacific white shrimp. J. Microbiol., 51: 695-699. 2013.   DOI
3 Hyatt, D., Chen, G.L., LoCascio, P.F., Land, M.L., Larimer, F.W. and Hauser, L.J.: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC bioinformatics, 11: 119. 2010.   DOI
4 Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., Rognes, T. and Ussery, D.W.: RNAmmer: consistent and rapid annotation of ribosomal RNA gene. Nucleic Acids Res., 35: 3100-3108. 2007.   DOI
5 Lee, D., Yu, Y.B., Choi, J.H., Jo, A.H., Hong, S.M., Kang, J.C. and Kim, J.H.: Viral shrimp diseases listed by the OIE: A review. Viruses, 14, 585, 2022.   DOI
6 Li, F., Gao, M., Xu, L. and Yang, F.: Comparative genomic analysis of three white spot syndrome virus isolates of different virulence. Virus Genes, 53: 249-258. 2017.   DOI
7 Ministry of oceans and fisheries (MOF): Survey on the current status of the seafood production and distribution industry in 2020. 2021b.
8 Ministry of oceans and fisheries (MOF). Aquatic life disease control Act. 2021a.
9 Oakey, H.J. and Smith, C.S.: Complete genome sequence of a white spot syndrome virus associated with a disease incursion in Australia. Aquaculture, 484: 152-159. 2018.   DOI
10 Office International des Epizooties (OIE).: Infection with white spot syndrome virus. Manual of diagnostic tests for aquatic animals. 2021.
11 Rodriguez-Anaya, L.Z., Gonzalez-Galaviz, J.R., Casillas-Hernandez, R., Lares-Villa, F., Estrada, K., Ibarra-Gamez, J.C. and Sanchez-Flores, A.: Draft genome sequence of white spot syndrome virus isolated from cultured Litopenaeus vannamei in Mexico. Genome Announc., 4: e01674-15. 2016.
12 Seemann, T.: Prokka: rapid prokaryotic genome annotation. Bioinformatics, 30: 2068-2069, 2014.   DOI
13 Bolger, A.M., Lohse, M. and Usadel, B.: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30: 2114-2120. 2014.   DOI
14 Jiang, L., Xiao, J., Liu, L., Pan, Y., Yan, S. and Wang, Y.: Characterization and prevalence of a novel white spot syndrome viral genotype in naturally infected wild crayfish, Procambarus clarkii, in Shanghai, China. VirusDis., 28: 250-261. 2017.   DOI
15 Laslett, D. and Canbak, B.: ARAGON, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res., 32: 11-16. 2004.   DOI
16 Lightner, D.V.: A handbook of shrimp pathology and diagnostic procedures for diseases of cultured penaeid shrimp. 1996.
17 National institute of fisheries science (NIFS). Standard manual of whiteleg shrimp culture. 2018.
18 Vargas-Albores, F., Hinojosa-Baltazar, P., Portillo-Clark, G. and Magallon-Barajas, F.: Influence of temperature and salinity on the yellowleg shrimp, Penaeus californieinsis Holmes, prophenoloxidase system. Aquaculture Res., 29: 549-553. 1998.   DOI
19 Vinaya Kumar, K., Shekhar, M.S., Otta, S.K., Karthic, K., Ashok Kumar, J. Gopikrishna, G. and Vijayan, K.K. First report of a complete genome sequence of white spot syndrome virus from India. Genome Announc., 6: e00055-18. 2018.
20 Tamura, K., Stecher, G. and Kumar, S.: MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol., 38: 3022-3027. 2021.   DOI
21 Restrepo, L., Reyes, A., Bajana, L., Betancourt, I. and Bayot, B.: Draft genome sequence of a white spot syndrome virus isolate obtained in Ecuador. Genome Announc., 6: e00605-18. 2018.
22 Kim, W.S., Oh, M.J., Jung, S.J., Kim, Y.J. and Kitamura, S.I.: Characterization of an iridovirus detected from cultured turbot, Scophthalmus maximus in Korea. Dis. Aquat. Org., 64: 175-180, 2005.   DOI