Bajaña, Leandro

Bayot, Bonny

Betancourt, Irma

Restrepo, Leda

Reyes, Alejandro

English

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Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2018Draft genome sequence of a white spot syndromevirus isolate obtained in EcuadorLeda RestrepoUniversidad de Los Andes - ColombiaAlejandro ReyesWashington University School of Medicine in St. LouisLeandro BajañaCentro Nacional de Acuicultura e Investigaciones Marinas, CENAIMIrma BetancourtCentro Nacional de Acuicultura e Investigaciones Marinas, CENAIMBonny BayotCentro Nacional de Acuicultura e Investigaciones Marinas, CENAIMFollow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubsThis Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in OpenAccess Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact engeszer@wustl.edu.Recommended CitationRestrepo, Leda; Reyes, Alejandro; Bajaña, Leandro; Betancourt, Irma; and Bayot, Bonny, ,"Draft genome sequence of a white spotsyndrome virus isolate obtained in Ecuador." Genome Announcements.6,26. e00605-18. (2018).https://digitalcommons.wustl.edu/open_access_pubs/7043Draft Genome Sequence of a White Spot Syndrome VirusIsolate Obtained in EcuadorLeda Restrepo,a,b,c Alejandro Reyes,b,c,d Leandro Bajaña,a Irma Betancourt,a Bonny Bayota,eaEscuela Superior Politécnica del Litoral (ESPOL), Centro Nacional de Acuicultura e Investigaciones Marinas,CENAIM, Guayaquil, EcuadorbDepartment of Biological Sciences, Universidad de los Andes, Bogotá, ColombiacMax Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, ColombiadCenter for Genome Sciences and Systems Biology, Department of Pathology and Immunology, WashingtonUniversity in Saint Louis, St. Louis, Missouri, USAeEscuela Superior Politécnica del Litoral (ESPOL), Facultad de Ingeniería Marítima, Ciencias Biológicas,Oceánicas y Recursos Naturales, FIMCBOR, Guayaquil, EcuadorABSTRACT White spot syndrome virus (WSSV) is the most devastating viral diseaseaffecting cultivated shrimp around the world. Currently, there is no reported geneticinformation on WSSV affecting Penaeus vannamei in Ecuador. Therefore, we deter-mined the genome of a WSSV isolate from shrimp and compared it with the ge-nomes of isolates from other geographical locations.Aquaculture is one of the most important economic activities in Ecuador, withPenaeus vannamei shrimp being the second highest nonoil export product, ac-counting for 95% of the country’s total aquaculture production (1). The presence of thepathogen white spot syndrome virus (WSSV) in Ecuador was conﬁrmed in 1999 (2). Insubsequent years, the disease became an epidemic, resulting in the virus being labeledas the most devastating pathogen in the aquacultural history of shrimp farming. Amonitoring effort was carried out along the Ecuadorian coast to evaluate the spread ofthe virus. Genotyping of the circulating WSSV types was performed to characterize thestrain diversity within the country, leading to the sequencing of the complete genomeof the most prevalent strain in this territory.A whole-genome sequencing (WGS) strategy was performed on an Illumina HiSeqsequencer using DNA extracted from infected shrimp containing strain WSSV-EC-15098.In total, 20,649,280 paired-end 2  101-bp reads were obtained, which generated2.085 Gb of total sequenced bases. The reads were mapped to the reference genomesof WSSV strain CN01 (3) (GenBank accession no. KT995472) and WSSV K-LV1 (4)(GenBank accession no. JX515788) using Bowtie 2 (5). They were then used for de novoassembly with SPAdes (6). The initial assembly generated 13 contigs. Reads mapping tothe edges of the contigs were extracted and assembled using CAP3 (7), and theresulting contigs were used to close the assembly, obtaining a single contig of288,997 bp. Open reading frames (ORFs) were predicted using the GeneMarkS software,with default parameters (8). The predicted protein sequences were searched againstthe GenBank database and the Clusters of Orthologous Groups (COGs) protein data-base using BLASTp (9).The draft genome of WSSV-EC-15098 consists of 288,997 bp, with a mean GCcontent of 40.92%. A total of 162 coding sequences (CDS) were predicted. The genomicarchitectures were compared with strains from China (3), Thailand (10), South Korea (4),and Mexico (11) using Mauve (12). A complete synteny among the assembled genomeswas observed. Two major deletions were observed in the WSSV-EC-15098 genome. Thedeletions were veriﬁed by paired-end reads located at each side of the deletion andReceived 28 May 2018 Accepted 30 May2018 Published 28 June 2018Citation Restrepo L, Reyes A, Bajaña L,Betancourt I, Bayot B. 2018. Draft genomesequence of a white spot syndrome virusisolate obtained in Ecuador. Genome Announc6:e00605-18. https://doi.org/10.1128/genomeA.00605-18.Copyright © 2018 Restrepo et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Leda Restrepo,ledarestrepoc@gmail.com.VIRUSEScrossmVolume 6 Issue 26 e00605-18 genomea.asm.org 1 on September 6, 2018 by guesthttp://mra.asm.org/Downloaded from mapping to the reference genome without any read mapping to any part of thedeleted segments. The deletions are a 3.24-kb fragment containing the ORFs VP22 andVP25, all annotated as envelope proteins, and a 17.04-kb fragment including the ORFVP35, annotated as a capsid protein. The deletion of proteins related to the envelopeis very interesting due to its potential role in modifying the way the virus interacts withthe host in terms of recognition of the host cell and by the immune machinery.Additionally, it has been observed that strain WSSC-EC-15098 is widely spread butcauses the lowest shrimp mortality rate.The average nucleotide identity (ANI) between WSSV-EC-15098 and other genomesis between 99.67% and 99.94%, with the WSSV-China genome being the most closelyrelated and WSSV-Korea genome being the most distantly related. The implementationof molecular epidemiology for the control of diseases could help in the developmentof strategies for the prevention and control of emerging and reemerging aquaculture-related diseases.Accession number(s). This whole-genome shotgun project has been deposited atDDBJ/EMBL/GenBank under the accession no. MH090824.ACKNOWLEDGMENTSWe thank Ana Elena Ayong for her technical help in this study and StanislausSonnenholzner for his kind reviewing of the manuscript and suggestions. Addition-ally, we acknowledge the High-Performance Computing Service at the Universidadde los Andes in Bogotá, Colombia, (http://hpc.uniandes.edu.co) for providing high-performance computing (HPC) resources that have contributed to the research resultsreported in this work.This work was funded by the Secretaria de Educación Superior, Ciencia, Tecnologíae Innovación (SENESCYT) in the framework of the PIC-14-CENAIM-003 project “Desar-rollo e implementación de métodos de control y prevención de enfermedades enespecies acuáticas de uso comercial y uso potencial en maricultura y repoblación.”REFERENCES1. Ministerio de Comercio Exterior. 2017. Pro Ecuador instituto de promociónde exportaciones e inversions. Ministerio de Comercio Exterior, Guayaquil,Ecuador. https://www.americaeconomia.com/economia-mercados/comercio/exportaciones-no-petroleras-de-ecuador-crecieron-77-y-suman-us10093m. (In Spanish.)2. Calderón J, Bayot B, Betancourt I, de Graindorge V. 1999. Monitoreo delvirus de la mancha blanca en Ecuador. El Mundo Acuícola 5:211–214.3. Yang F, He J, Lin X, Li Q, Pan D, Zhang X, Xu X. 2001. Complete genomesequence of the shrimp white spot bacilliform virus. J Virol 75:11811–11820.https://doi.org/10.1128/JVI.75.23.11811-11820.2001.4. Chai C, Yoon J, Lee Y, Kim Y, Choi T. 2013. Analysis of the completenucleotide sequence of a white spot syndrome virus isolated from Paciﬁcwhite shrimp. J Microbiol 51:695–699. https://doi.org/10.1007/s12275-013-3171-0.5. Langmead B, Salzberg S. 2012. Fast gapped-read alignment with Bowtie2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923.6. Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A, LesinV, Nikolenko S, Pham S, Prjibelski A, Pyshkin A, Sirotkin A, Vyahhi N,Tesler G, Alekseyev M, Pevzner P. 2012. SPAdes: a new genome assemblyalgorithm and its applications to single-cell sequencing. J Comput Biol19:455–477. https://doi.org/10.1089/cmb.2012.0021.7. Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program.Genome Res 9:868–877. https://doi.org/10.1101/gr.9.9.868.8. Besemer J, Borodovsky M. 2005. GeneMark: Web software for gene ﬁndingin prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454.https://doi.org/10.1093/nar/gki487.9. Tatusov R, Galperin M, Natale D, Koonin E. 2000. The COG database: atool for genome-scale analysis of protein functions and evolution. Nu-cleic Acids Res 28:33–36. https://doi.org/10.1093/nar/28.1.33.10. Van Hulten M, Witteveldt J, Peters S, Kloosterboer N, Tarchini R, Fiers M,Sandbrink H, Lankhorst R, Vlak J. 2001. The white spot syndrome virusDNA genome sequence. Virology 286:7–22. https://doi.org/10.1006/viro.2001.1002.11. Rodriguez-Anayaa LZ, Gonzalez-Galaviza JR, Casillas-Hernandeza R,Lares-Villaa F, Estradab K, Ibarra-Gameza JC, Sanchez-Flores A. 2016.Draft genome sequence of white spot syndrome virus isolated fromcultured Litopenaeus vannamei in Mexico. Genome Announc 4:e01674-15. https://doi.org/10.1128/genomeA.01674-15.12. Darling ACE, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple align-ment of conserved genomic sequence with rearrangements. GenomeRes 14:1394–1403. https://doi.org/10.1101/gr.2289704.Restrepo et al.Volume 6 Issue 26 e00605-18 genomea.asm.org 2 on September 6, 2018 by guesthttp://mra.asm.org/Downloaded from 

Draft genome sequence of a white spot syndrome virus isolate obtained in Ecuador

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Draft genome sequence of a white spot syndrome virus isolate obtained in Ecuador

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