Vibrio species of the Harveyi clade are commonly found in free-living and host-associated marine habitats. Here, we report the draft genome sequence for a Harveyi clade bacterium, Vibrio sp. strain LB10LO1, which was isolated from the Atlantic brief squid Lolliguncula brevis

Coleman, C.K.

Dorsey, C.

Gifford, S.M.

Septer, A.N.

Smith, S.

Speare, L.

Wilson, T.

Carolina Digital Repository

Draft Genome Sequence of a Harveyi Clade Bacterium Isolatedfrom Lolliguncula brevis SquidAlecia N. Septer,a Lauren Speare,a Collin K. Coleman,b Stephanie Smith,a Coby Dorsey,a Travis Wilson,a Scott M. GiffordaaDepartment of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, USAbDepartment of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina, USAABSTRACT Vibrio species of the Harveyi clade are commonly found in free-livingand host-associated marine habitats. Here, we report the draft genome sequence fora Harveyi clade bacterium, Vibrio sp. strain LB10LO1, which was isolated from the At-lantic brief squid Lolliguncula brevis.Bacteria within the genus Vibrio are widely distributed throughout marine systemswhere they inhabit both nutrient-rich and oligotrophic environments (1). Withinthe Vibrio genus, members of the Harveyi clade include 11 closely related species thatare commonly found in surface waters, in marine sediments, and as pathogens andcommensals of both vertebrates and invertebrates (2–13). Moreover, these speciesserve as important model organisms for studying biofilm formation, bioluminescence,and quorum sensing (14).Here, we introduce the genome sequence of a Harveyi clade bacterium, Vibrio sp.strain LB10LO1, which was isolated from a wild-caught Atlantic brief squid, Lolligunculabrevis. In the summer of 2017, L. brevis squid were collected from the bycatch of a trawloff the coast of Morehead City, North Carolina. A deceased animal was immediatelywashed with filter-sterilized instant ocean. Tissue within the mantle cavity was re-moved, homogenized, and plated directly onto Luria-Bertani with added salt (LBS) agar(15). Cultivation plates were incubated at 24°C overnight, and a brightly luminescentcolony was picked and restreaked for purification, resulting in strain LB10LO1. Theinitial phylogeny of this isolate was determined using analysis of the hsp60 and toxRsequences (16, 17), which suggested that LB10LO1 is a Vibrio campbellii species withinthe Harveyi clade. Because recent studies have shown that whole-genome comparisonsare the best way to confirm phylogeny among Harveyi clade members (2), we soughtto sequence the genome of LB10LO1 to determine how this isolate relates to otherspecies within the Harveyi clade.A single LB10LO1 colony was picked and streaked onto LBS agar plates andincubated overnight at 24°C. Genomic DNA was extracted from this clonal bacterialgrowth with a Zymo DNA miniprep kit, and the quantity and quality were determinedusing an Eppendorf BioSpectrometer. Library preparation was performed using aTruSeq DNA kit (Illumina, San Diego, CA, USA), following the manufacturer’s protocol.The library was sequenced using the MiSeq Illumina platform and 300-bp paired-endreads at the University of North Carolina (UNC) High-Throughput Genomic SequencingFacility, resulting in a total of 1,798,287 paired reads. Raw reads were trimmed usingTrimmomatic (18) using a 10-bp sliding window average, Phred score threshold of 20,and minimum read length of 50 nucleotides (nt). Paired reads were assembled usingPEAR (default settings) (19). The remaining sequences were assembled using SPAdes(default settings) (20); sequences were annotated via the Prokka Prokaryotic GenomeAnnotation Pipeline, BlastKoala within the KEGG platform, and BioCyc (21).The final draft genome of LB10LO1 is 5,515,790 bp long in 90 contigs (1,000 bp),Citation Septer AN, Speare L, Coleman CK,Smith S, Dorsey C, Wilson T, Gifford SM. 2020.Draft genome sequence of a Harveyi cladebacterium isolated from Lolliguncula brevissquid. Microbiol Resour Announc 9:e00078-20.https://doi.org/10.1128/MRA.00078-20.Editor Frank J. Stewart, Georgia Institute ofTechnologyCopyright © 2020 Septer et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Alecia N. Septer,asepter@email.unc.edu, or Scott M. Gifford,sgifford@email.unc.edu.Received 27 January 2020Accepted 29 January 2020Published 20 February 2020GENOME SEQUENCEScrossmVolume 9 Issue 8 e00078-20 mra.asm.org 1with a GC content of 45.45%, 97-fold genome coverage, and an N50 score of165,319 bp. A total of 4,995 DNA coding regions were identified, including 4,891encoding proteins and 104 encoding RNAs. Prokka produced annotated functions for3,127 of the proteins, while the other 1,764 proteins were assigned as hypothetical.Finally, a MiGA (22) and Genome Taxonomy Database (GTDB) (23) analysis of theLB10LO1 genome determined that the most closely related genomes in the databasewere Vibrio campbellii isolates, with an average nucleotide identity (ANI) of 96%.Data availability. This genome sequence is available in GenBank under the Bio-Project number PRJNA602499; the Illumina reads are available in the SRA underaccession number SRX7614634. Cultures of LB10LO1 are available upon request.ACKNOWLEDGMENTSThis work was supported by a UNC Course-based Undergraduate Research Experi-ence (CURE) award to S.M.G. C.D. was supported by the UNC Institute for the Environ-ment’s IDEA program (NSF number 1600506). C.K.C. was supported in part by a grantfrom the National Institute of Environmental Health Sciences (T32ES007018).We thank Acacia Zhao for technical assistance and Joel Fodrie, Martin Benavides,and the crew of the R/V Capricorn for assistance in the field.REFERENCES1. Thompson JR, Polz MF. 2006. Dynamics of Vibrio populations and theirrole in environmental nutrient cycling, p 190 –203. In Thompson FL,Austin B, Swings J (eds), Biology of vibrios. ASM Press, Washington, DC.2. Urbanczyk H, Ogura Y, Hayashi T. 2013. Taxonomic revision of Harveyiclade bacteria (family Vibrionaceae) based on analysis of whole genomesequences. Int J Syst Evol Microbiol 63:2742–2751. https://doi.org/10.1099/ijs.0.051110-0.3. 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Draft genome sequence of a harveyi clade bacterium isolated from lolliguncula brevis squid

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Draft genome sequence of a harveyi clade bacterium isolated from lolliguncula brevis squid

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