# Draft Genome Sequence of the Fish Pathogen
Flavobacterium columnare Genomovar III Strain
PH-97028 (=CIP 109753)

Alexis Criscuolo, Olivier Chesneau, Dominique Clermont, Chantal Bizet

► To cite this version:

Alexis Criscuolo, Olivier Chesneau, Dominique Clermont, Chantal Bizet. Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753). Genome Announcements, 2018, 6 (14), pp.e00222-18. 10.1128/genomeA.00222-18. pasteur-03082421

HAL Id: pasteur-03082421

https://pasteur.hal.science/pasteur-03082421

Submitted on 18 Dec 2020

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_2.png" /></figure>

# Draft Genome Sequence of the Fish Pathogen *Flavobacterium columnare* Genomovar III Strain PH-97028 (=CIP 109753)

Alexis Criscuolo,ª Olivier Chesneau,ᵇ Dominique Clermont,ᵇ Chantal Bizetᵇ

**ABSTRACT** *Flavobacterium columnare* strain PH-97028 (=CIP 109753) is a genomovar III reference strain that was isolated from a diseased Ayu fish in Japan. We report here the analysis of the first available genomovar III sequence of this species to aid in identification, epidemiological tracking, and virulence studies.

There is a high genetic heterogeneity within the species *Flavobacterium columnare*, a yellow-colored, Gram-negative, rod-shaped bacterium that is known as the etiologic agent of columnaris disease in freshwater fish. Despite diverse hosts and disease outbreaks worldwide, *F. columnare* isolates cannot be phenotypically distinguished, and subcategorization relies on three clades or genotypes whose rRNA gene is the support (1). As of February 2018, only 15 genomes of *F. columnare* isolates are publicly available, among which, representative ones belong to only genomovar I (e.g., strains ATCC 49512 and Pf1) or II (e.g., strains C#2 and 94-081) (2). Here, we report the first genome assembly of a representative strain from *F. columnare* genomovar III, strain PH-97028 (=CIP 109753), for which no functional data have been analyzed thus far.

A single colony of strain PH-97028 was grown overnight in 10 ml of CIP medium 469 (10 g peptone, 10 g yeast extract, 5 g sodium chloride, and 1 liter distilled water) at 30°C with shaking for 24 h. Total cellular DNA was obtained from 2 ml of culture using the Wizard genomic DNA purification kit (Promega, Madison, WI, USA). Libraries were constructed using the Nextera XT DNA library preparation kit (Illumina, Inc., San Diego, CA, USA) and sequenced on a NextSeq 500 instrument using a 2 × 150-bp paired-end protocol, leading to 1,409,297 read pairs (>120× average sequencing depth, ~250 bp insert size).

Sequenced reads were clipped and trimmed with AlienTrimmer (3) and corrected with Musket (4). The remaining processed reads were assembled and scaffolded with SPAdes (5). The draft genome has a total size of 3,255,527 bp, represented in 204 scaffolds, with an N<sub>50</sub> value of 51,970 bp. Its G+C content of 30.66% is slightly lower than the G+C content of genomovar I and II genomes (e.g., 31.5% and 30.9%, respectively). Scaffold sequences were processed with Prokka (6) for gene prediction and annotation, which led to the detection of 2,727 coding genes and 41 tRNAs.

Functional genome analysis of strain PH-97028 revealed the presence of orthologs of the *F. johnsoniae* genes *gldK*, *gldL*, *gldM*, *gldN*, *sprA*, *sprE*, *sprT*, *porU*, and *porV*. The proteins encoded by these genes are components of the type IX secretion system machinery that was shown to be involved in gliding motility and virulence properties for several members of the phylum *Bacteroidetes* (7). In addition to numerous toxins and mobile elements, and contrary to the *F. columnare* genomovar I and II genomes, the genome of strain PH-97028 would encode a group II intron reverse transcriptase/ maturase and a complete HemTUV ATP-binding cassette system.

The two-way average nucleotide identity values between *F. columnare* strain PH-97028 (genomovar III) and *F. columnare* representative strains from genomovars I and

Received 21 February 2018 Accepted 16

March 2018 Published 5 April 2018

**Citation** Criscuolo A, Chesneau O, Clermont D, Bizet C. 2018. Draft genome sequence of the fish pathogen *Flavobacterium columnare* genomovar III strain PH-97028 (=CIP 109753). Genome Announc 6:e00222-18. https://doi.org/10.1128/genomeA.00222-18.

**Copyright** © 2018 Criscuolo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Olivier Chesneau, olivier.chesneau@pasteur.fr.

<footnote>ªInstitut Pasteur, Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP CNRS, Paris, France</footnote>

<footnote>ᵇMicrobiology Department, Institut Pasteur, Collection de l'Institut Pasteur, Paris, France</footnote>
It vary from 85.09% to 85.60%, respectively, confirming that strain PH-97028 belongs to a third distinct genomovar within the species.

**Accession number(s).** This whole-genome shotgun project has been deposited at the European Nucleotide Archive (ENA) under the sequencing project number PRJEB25044. Scaffold sequences and annotations were deposited at DDBJ/EMBL/GenBank under the accession number **OLKH00000000**. The version described in this paper is the first version, OLKH01000000.

## ACKNOWLEDGMENTS

We thank the Mutualized Microbiology Platform (P2M) of the Pasteur International Bioresources Network (PIBnet) of the Institut Pasteur, Paris, France, for assistance with whole-genome sequencing.

This work received no specific grant from any funding agency.

## REFERENCES

1. Kayansamruaj P, Dong HT, Hirono I, Kondo H, Senapin S, Rodkhum C. 2017. Comparative genome analysis of fish pathogen *Flavobacterium columnare* reveals extensive sequence diversity within the species. *Infect Genet Evol* 54:7–17. https://doi.org/10.1016/j.meegid.2017.06.012.

2. Kumru S, Tekedar HC, Gulsoy N, Waldbieser GC, Lawrence ML, Karsi A. 2017. Comparative analysis of the *Flavobacterium columnare* genomovar I and II genomes. *Front Microbiol* 8:1315. https://doi.org/10.3389/fmicb.2017.01375.

3. Criscuolo A, Brisse S. 2013. AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. *Genomics* 102:500–506. https://doi.org/10.1016/j.ygeno.2013.07.011.

4. Liu Y, Schröder J, Schmidt B. 2013. Musket: a multistage *k*-mer spectrum-based error corrector for Illumina sequence data. *Bioinformatics* 29: 308–315. https://doi.org/10.1093/bioinformatics/bts690.

5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. *J Comput Biol* 19:455–477. https://doi.org/10.1089/cmb.2012.0021.

6. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153.

7. Li N, Zhu Y, LaFrentz BR, Evenhuis JP, Hunnicutt DW, Conrad RA, Barbier P, Gullstrand CW, Roets JE, Powers JL, Kulkarni SS, Erbes DH, García JC, Nie P, McBride MJ. 2017. The type IX secretion system is required for virulence of the fish pathogen *Flavobacterium columnare*. *Appl Environ Microbiol* 83:e01769-17. https://doi.org/10.1128/AEM.01769-17.