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Prokaryotes

Three Draft Genome Sequences of Vibrio coralliilyticus Strains Isolated from Bivalve Hatcheries

Hanna Kehlet-Delgado, Gary P. Richards, Claudia Häse, Ryan S. Mueller
Hanna Kehlet-Delgado
a Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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Gary P. Richards
b U.S. Department of Agriculture, Agricultural Research Service, Dover, Delaware, USA
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Claudia Häse
c Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
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Ryan S. Mueller
a Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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DOI: 10.1128/genomeA.01162-17
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ABSTRACT

Reported here are the genome sequences of three Vibrio coralliilyticus isolates RE87, AIC-7, and 080116A. Each strain was isolated in association with oyster larvae in commercial aquaculture systems. These draft genomes will be useful for further studies in understanding the genomic features contributing to V. coralliilyticus pathogenicity.

GENOME ANNOUNCEMENT

Vibrio coralliilyticus is a known pathogen of corals (1) and shellfish, including Pacific oyster (Crassostrea gigas) larvae (2–5). In order to further the understanding of the genomic repertoire of V. coralliilyticus, particularly isolates pathogenic to oyster larvae, we sequenced three strains isolated from oyster aquaculture facilities. Strain RE87 was isolated in 2000 from dying C. gigas seed at a Hawaii nursery. Strain AIC-7 was isolated from a vibriosis outbreak among Eastern oysters (Crassostrea virginica) in 2015 at a hatchery in New Jersey. Strain 080116A was isolated in 2016 from C. gigas larvae tanks at an Oregon hatchery. All three strains demonstrated a degree in pathogenicity in preliminary pathogenicity challenges with C. gigas larvae (80 to 100% larval mortalities after 48 h [our unpublished data]).

DNA from overnight cultures was isolated and the Nextera XT kit (Illumina) was used to prepare libraries for sequencing on a MiSeq Illumina platform at the Center for Genome Research and Biocomputing at Oregon State University. Each genome library was sequenced with 250-bp paired-end reads at an estimated minimum coverage of 65-fold. The resulting reads were trimmed and quality filtered (Q > 28, minimum read length 150 bp) using Sickle (6) and randomly subsampled to an estimated coverage of 50-fold. Reads were subsequently de novo assembled using IDBA-UD (7). The assembly for strain RE87 had a genome size of 5.59 Mbp (45.8% GC), 49 contigs (N50 = 335,391 bp), and a maximum contig size of 1,074,445 bp; the assembly for strain AIC-7 resulted in a genome size of 5.95 Mbp (45.3% GC), 65 contigs (N50 = 274,060 bp), and a maximum contig size of 1,201,114 bp; and the assembly for strain 080116A had a genome size of 5.63 Mb (45.7% GC), 107 contigs (N50 = 275,484 bp), and a maximum contig size of 1,249,611 bp.

Gene predictions for the draft assemblies were performed using Prokka version 1.11 (8) and Rapid Annotation using Subsystem Technology (RAST) (9). There were 5,145, 5,542, and 5,205 coding sequences detected for strains RE87, AIC-7, and 080116A, respectively. Proteinortho (10) detected 1,813 orthologous clusters that were shared among the three isolates, representing 57 to 62% of the predicted proteome of each genome. Strain RE87 has 266 unique genes, AIC-7 has 504, and 080116A has 287. To compare genome similarities with other V. coralliilyticus strains, average nucleotide identities (ANI) were calculated using Enviomics (11). ANI values for each strain with V. coralliilyticus strains ATCC BAA-450 (12), RE98 (13), OCN014 (14), and 58 (15) were >96%, corresponding to grouping at the species level (16, 17). All three strains had open reading frames displaying 99% homology to the VtpA extracellular zinc metalloprotease of V. coralliilyticus RE98, a known virulence factor for C. gigas (18). A more in-depth genomic analysis of these and other V. coralliilyticus strains will be conducted for a future publication.

Accession number(s).This whole-genome shotgun project has been deposited in GenBank under the accession numbers NRHY00000000 (RE87), NRQO00000000 (AIC-7), and NRHV00000000 (080116A). The versions described in this paper are the first versions.

ACKNOWLEDGMENTS

This study was funded by Agriculture and Food Research Initiative grant 2015-08632 of the USDA National Institute of Food and Agriculture.

The use of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.

We thank Mark Dasenko at the Center for Genome Research Biocomputing at Oregon State University for help with library preparation and sequencing and David Madison for advice regarding pathogenicity tests.

FOOTNOTES

    • Received 14 September 2017.
    • Accepted 18 September 2017.
    • Published 12 October 2017.
  • Copyright © 2017 Kehlet-Delgado et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license .

REFERENCES

  1. 1.↵
    1. Ben-Haim Y,
    2. Thompson FL,
    3. Thompson CC,
    4. Cnockaert MC,
    5. Hoste B,
    6. Swings J,
    7. Rosenberg E
    . 2003. Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis. Int J Syst Evol Microbiol53:309–315. doi:10.1099/ijs.0.02402-0.
    OpenUrlCrossRefPubMedWeb of Science
  2. 2.↵
    1. Elston RA,
    2. Hasegawa H,
    3. Humphrey KL,
    4. Polyak IK,
    5. Häse CC
    . 2008. Re-emergence of Vibrio tubiashii in bivalve shellfish aquaculture: severity, environmental drivers, geographic extent and management. Dis Aquat Organ82:119–134. doi:10.3354/dao01982.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Richards GP,
    2. Watson MA,
    3. Needleman DS,
    4. Church KM,
    5. Häse CC
    . 2015. Mortalities of Eastern and Pacific oyster larvae caused by the pathogens Vibrio coralliilyticus and Vibrio tubiashii. Appl Environ Microbiol81:292–297. doi:10.1128/AEM.02930-14.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Kesarcodi-Watson A,
    2. Miner P,
    3. Nicolas J-L,
    4. Robert R
    . 2012. Protective effect of four potential probiotics against pathogen-challenge of the larvae of three bivalves: Pacific oyster (Crassostrea gigas), flat oyster (Ostrea edulis) and scallop (Pecten maximus). Aquaculture344:29–34.
    OpenUrl
  5. 5.↵
    1. Genard B,
    2. Miner P,
    3. Nicolas JL,
    4. Moraga D,
    5. Boudry P,
    6. Pernet F,
    7. Tremblay R
    . 2013. Integrative study of physiological changes associated with bacterial infection in Pacific oyster larvae. PLoS One8:e64534. doi:10.1371/journal.pone.0064534.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Joshi NA,
    2. Fass JN
    . Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. https://github.com/najoshi/sickle .
  7. 7.↵
    1. Peng Y,
    2. Leung HCM,
    3. Yiu SM,
    4. Chin FYL
    . 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics28:1420–1428. doi:10.1093/bioinformatics/bts174.
    OpenUrlCrossRefPubMedWeb of Science
  8. 8.↵
    1. Seemann T
    . 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics30:2068–2069. doi:10.1093/bioinformatics/btu153.
    OpenUrlCrossRefPubMedWeb of Science
  9. 9.↵
    1. Overbeek R,
    2. Olson R,
    3. Pusch GD,
    4. Olsen GJ,
    5. Davis JJ,
    6. Disz T,
    7. Edwards RA,
    8. Gerdes S,
    9. Parrello B,
    10. Shukla M,
    11. Vonstein V,
    12. Wattam AR,
    13. Xia F,
    14. Stevens R
    . 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res42:D206–D214. doi:10.1093/nar/gkt1226.
    OpenUrlCrossRefPubMedWeb of Science
  10. 10.↵
    1. Lechner M,
    2. Findeiss S,
    3. Steiner L,
    4. Marz M,
    5. Stadler PF,
    6. Prohaska SJ
    . 2011. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics12:124. doi:10.1186/1471-2105-12-124.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Rodriguez-R LM,
    2. Konstantinidis KT
    . 2016. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints4:e1900v1.
    OpenUrlCrossRef
  12. 12.↵
    1. Kimes NE,
    2. Grim CJ,
    3. Johnson WR,
    4. Hasan NA,
    5. Tall BD,
    6. Kothary MH,
    7. Kiss H,
    8. Munk AC,
    9. Tapia R,
    10. Green L,
    11. Detter C,
    12. Bruce DC,
    13. Brettin TS,
    14. Colwell RR,
    15. Morris PJ
    . 2012. Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. ISME J6:835–846. doi:10.1038/ismej.2011.154.
    OpenUrlCrossRefPubMedWeb of Science
  13. 13.↵
    1. Richards GP,
    2. Bono JL,
    3. Watson MA,
    4. Needleman DS
    . 2014. Complete genome sequence for the shellfish pathogen Vibrio coralliilyticus RE98 isolated from a shellfish hatchery. Genome Announc2(6):e01253-14. doi:10.1128/genomeA.01253-14.
    OpenUrlAbstract/FREE Full Text
  14. 14.↵
    1. Ushijima B,
    2. Videau P,
    3. Poscablo D,
    4. Vine V,
    5. Salcedo M,
    6. Aeby G,
    7. Callahan SM
    . 2014. Complete genome sequence of Vibrio coralliilyticus strain OCN014, isolated from a diseased coral at Palmyra Atoll. Genome Announc2(6):e01318-14. doi:10.1128/genomeA.01318-14.
    OpenUrlAbstract/FREE Full Text
  15. 15.↵
    1. Kim HJ,
    2. Kim JH,
    3. Jun JW,
    4. Giri SS,
    5. Chi C,
    6. Yun S,
    7. Kim SG,
    8. Kim SW,
    9. Kang JW,
    10. Jeong DG,
    11. Park SC
    . 2017. Complete genome sequence of Vibrio coralliilyticus 58, Isolated from Pacific oyster (Crassostrea gigas) larvae. Genome Announc5(23):e00437-17. doi:10.1128/genomeA.00437-17.
    OpenUrlAbstract/FREE Full Text
  16. 16.↵
    1. Goris J,
    2. Konstantinidis KT,
    3. Klappenbach JA,
    4. Coenye T,
    5. Vandamme P,
    6. Tiedje JM
    . 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol57:81–91. doi:10.1099/ijs.0.64483-0.
    OpenUrlCrossRefPubMedWeb of Science
  17. 17.↵
    1. Kim M,
    2. Oh HS,
    3. Park SC,
    4. Chun J
    . 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol64:346–351. doi:10.1099/ijs.0.059774-0.
    OpenUrlCrossRefPubMedWeb of Science
  18. 18.↵
    1. Hasegawa H,
    2. Lind EJ,
    3. Boin MA,
    4. Häse CC
    . 2008. The extracellular metalloprotease of Vibrio tubiashii Is a major virulence factor for Pacific oyster (Crassostrea gigas) larvae. Appl Environ Microbiol74:4101–4110. doi:10.1128/AEM.00061-08.
    OpenUrlAbstract/FREE Full Text
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Three Draft Genome Sequences of Vibrio coralliilyticus Strains Isolated from Bivalve Hatcheries
Hanna Kehlet-Delgado, Gary P. Richards, Claudia Häse, Ryan S. Mueller
Genome Announcements Oct 2017, 5 (41) e01162-17; DOI: 10.1128/genomeA.01162-17

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Three Draft Genome Sequences of Vibrio coralliilyticus Strains Isolated from Bivalve Hatcheries
Hanna Kehlet-Delgado, Gary P. Richards, Claudia Häse, Ryan S. Mueller
Genome Announcements Oct 2017, 5 (41) e01162-17; DOI: 10.1128/genomeA.01162-17
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