Vibrio tubiashii subsp. europaeus is a bivalve pathogen isolated during episodes of mortality affecting larval cultures in different shellfish hatcheries. Here, we announce the draft genome sequence of the type strain PP-638 and describe potential virulence factors, which may provide insight into the mechanism of pathogenicity

Barja, Juan L

Dubert, Javier

Gomez-Chiarri, Marta

Nelson, David R.

Spinard, Edward J

English

PubMed

DigitalCommons@URI

University of Rhode IslandDigitalCommons@URICell and Molecular Biology Faculty Publications Cell and Molecular Biology2016Draft Genome Sequence of the Emerging BivalvePathogen Vibrio tubiashii subsp. europaeusEdward J. SpinardJavier DubertSee next page for additional authorsCreative Commons LicenseCreative Commons LicenseThis work is licensed under a Creative Commons Attribution 4.0 License.Follow this and additional works at: https://digitalcommons.uri.edu/cmb_facpubsThis Article is brought to you for free and open access by the Cell and Molecular Biology at DigitalCommons@URI. It has been accepted for inclusionin Cell and Molecular Biology Faculty Publications by an authorized administrator of DigitalCommons@URI. For more information, please contactdigitalcommons@etal.uri.edu.Citation/Publisher AttributionSpinard, E. J., Dubert, J., Nelson, D. R., Gomez-Chiarri, M., and Barja, J. L. (2016). Draft genome sequence of the emerging bivalvepathogen Vibrio tubiashii subsp. europaeus. Genome Announcements, 4 (4): e00625-16. doi: 10.1128/genomeA.00625-16Available at: http://dx.doi.org/10.1128/genomeA.00625-16AuthorsEdward J. Spinard, Javier Dubert, David R. Nelson, Marta Gomez-Chiarri, and Juan L. BarjaThis article is available at DigitalCommons@URI: https://digitalcommons.uri.edu/cmb_facpubs/33Draft Genome Sequence of the Emerging Bivalve Pathogen Vibriotubiashii subsp. europaeusEdward J. Spinard,a Javier Dubert,b David R. Nelson,a Marta Gomez-Chiarri,c Juan L. BarjabDepartment of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USAa; Departamento de Microbiología y Parasitología, CIBUS, Facultad deBiología, Universidade de Santiago de Compostela, Santiago de Compostela, Spainb; Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island,Kingston, Rhode Island, USAcVibrio tubiashii subsp. europaeus is a bivalve pathogen isolated during episodes of mortality affecting larval cultures in differentshellfish hatcheries. Here, we announce the draft genome sequence of the type strain PP-638 and describe potential virulencefactors, which may provide insight into the mechanism of pathogenicity.Received 10 May 2016 Accepted 10 June 2016 Published 28 July 2016Citation Spinard EJ, Dubert J, Nelson DR, Gomez-Chiarri M, Barja JL. 2016. Draft genome sequence of the emerging bivalve pathogen Vibrio tubiashii subsp. europaeus.Genome Announc 4(4):e00625-16. doi:10.1128/genomeA.00625-16.Copyright © 2016 Spinard et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to David R. Nelson, dnelson@uri.edu.Vibrio tubiashii subsp. europaeus is an emerging bivalve patho-gen identified recently as the etiological agent responsible forlarval and spat mortalities in clam, oyster, and abalone culturesdetected in Spanish and French hatcheries (1, 2). This pathogen isa causative agent of vibriosis, inducing mass mortalities and im-portant economic losses, representing themain bottleneck for theproduction process in shellfish aquaculture (1, 2).V. tubiashii subsp. europaeus PP-638T (CECT 8136TDSM27349T) was originally isolated from a culture tank of flat oyster(Ostrea edulis) during an episode of larval mortality in a shellfishhatchery (Galicia, Northwest Spain) (1). DNA was isolated fromV. tubiashii subsp. europaeus PP-638T grown overnight in YP30using the Wizard genomic DNA purification kit (Promega), ac-cording the manufacturer’s instructions, except DNA was resus-pended in 2 mM Tris-HCl buffer (Bio Basic). Genomic DNA wassequenced using an Illumina MiSeq at the Genomics and Se-quencing Center at the University of Rhode Island, Kingston, RI.Reads were trimmed using CLC Genomics Workbench (version8.5.1) for quality, ambiguous nucleotides, and adapters. A total of2,943,708 paired-end and 3,234,516 mate-paired reads providing199 coverage were assembled using SPAdes (version 3.1.1), usingdefault parameters (3). Contigs were filtered based on 34 coverageand 4,000-bp length, resulting in 10 contigs with anN50 of 1,788,614and an average GC content of 45.37%. The assembly was mappedto Vibrio tubiashii ATCC 19109 using the CLC Microbial GenomeFinishing module and resulted in six contigs mapping to chromo-some 1, one complete contig representing chromosome 2, one com-plete contig representing the p251-likemegaplasmid, and one contigmapping to the p57-like plasmid (4). One 4,885-bp contig did notmap to the reference genome. The draft genome was submitted toRapid Annotations using Subsystems Technology (RAST) for anno-tation, resulting in 5,157 open reading frames (5–7).Encoded on chromosome 2 of theV. tubiashii subsp. europaeusPP-638T genome is a putativemetalloproteasewith 75% similarityto VtpA found in Vibrio coralliilyticus RE22 (8). Another proteasewith 71% similarity to Epp in Vibrio anguillarum M93Sm is en-coded on chromosome 2 (9). Three putative hemolysins andphospholipases are encoded in the genome. One hemolysin lo-cated on chromosome 2 has 67% similarity to Plp in V. anguilla-rumM93Sm (10, 11). InV. anguillarumM93Sm, plp is divergentlytranscribed from the pore-forming hemolysin/cytolysin vah1(11). InV. tubiashii subsp. europaeus PP-638T, the Plp homolog isalso divergently transcribed away from a pore-forming cytolysin,although it has 42% similarity to aerolysin in Aeromonas eucreno-phila (NCBI Reference Sequence WP_042642875.1), not vah1.The genomeencodes two secretion systems (type III secretion system[T3SS] and T6SS) that are used to deliver effector molecules directlyinto the host. The T3SS-secreted virulence factor has a domain simi-lar to the GTPase-activating domain found on YopE from Yersiniapestis (12–16).While theT6SSstructural components are encodedonthe p251-like megaplasmid, the protein responsible for forming thepuncturing tip of the T6SS secretion system, VgrG, appears to beencoded by two genes. One VgrG-encoding gene is on chromosome1, and the second is on chromosome 2.Nucleotide sequence accessionnumbers.Thiswhole-genomeshotgun project has been deposited inDDBJ/EMBL/GenBank un-der the accession no. LUAX00000000. The version described inthis paper is the first version LUAX01000000.ACKNOWLEDGMENTSThis material is based upon work conducted at a Rhode Island NSF EPS-CoR research facility, the Genomics and Sequencing Center, supported inpart by the National Science Foundation EPSCoR Cooperative Agree-ment no. EPS-1004057 and by grant AGL2014–59655 from the Ministryof Economy and Competitiveness of Spain.FUNDING INFORMATIONThis work, including the efforts of Juan L. Barja, was funded byMinistry of Economy and Competiveness of Spain (AGL2014-59655).The funders had no role in study design, data collection and interpreta-tion, or the decision to submit the work for publication.crossmarkGenome AnnouncementsJuly/August 2016 Volume 4 Issue 4 e00625-16 genomea.asm.org 1 on August 31, 2017 by UNIV OF RHODE ISLANDhttp://genomea.asm.org/Downloaded from REFERENCES1. Prado S, Dubert J, Barja JL. 2015. Characterization of pathogenic vibriosisolated from bivalve hatcheries in Galicia, NW Atlantic coast of Spain.Description of Vibrio tubiashii subsp. europaensis subsp. nov. Syst ApplMicrobiol 38:26–29. http://dx.doi.org/10.1016/j.syapm.2014.11.005.2. Travers MA, Mersni Achour R, Haffner P, Tourbiez D, Cassone AL,Morga B, Doghri I, Garcia C, Renault T, Fruitier-Arnaudin I, SaulnierD. 2014. 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Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, OlsonR, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T,Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V,Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations usingSubsystems Technology. BMCGenomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.6. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R,Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA, III,Stevens R, Vonstein V, Wattam AR, Xia F. 2015. RASTtk: a modular andextensible implementation of the RAST algorithm for building customannotation pipelines and annotating batches of genomes. Sci Rep 5:8365.http://dx.doi.org/10.1038/srep08365.7. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, EdwardsRA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F,Stevens R. 2014. 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Draft Genome Sequence of the Emerging Bivalve Pathogen \u3cem\u3eVibrio tubiashii\u3c/em\u3e subsp. \u3cem\u3eeuropaeus\u3c/em\u3e

ABSTRACT
          
            Vibrio tubiashii
            subsp.
            europaeus
            is a bivalve pathogen isolated during episodes of mortality affecting larval cultures in different shellfish hatcheries. Here, we announce the draft genome sequence of the type strain PP-638 and describe potential virulence factors, which may provide insight into the mechanism of pathogenicity.
          </jats:p

Edward J. Spinard

Javier Dubert

David R. Nelson

Marta Gomez-Chiarri

Juan L. Barja

Crossref

Genome Announcements

Draft Genome Sequence of the Emerging Bivalve Pathogen
            <i>Vibrio tubiashii</i>
            subsp.
            <i>europaeus</i>

https://digitalcommons.uri.edu/cgi/viewcontent.cgi?article=1034&amp;context=cmb_facpubs

Draft Genome Sequence of the Emerging Bivalve Pathogen \u3cem\u3eVibrio tubiashii\u3c/em\u3e subsp. \u3cem\u3eeuropaeus\u3c/em\u3e

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