Complete Genome Sequence of Lacinutrix venerupis DOK2-8 Isolated from Marine Sediment from the East Sea, Republic of Korea

ABSTRACT

Lacinutrix venerupis has recently been considered a potential fish pathogen. Here, we report the complete genome sequence of L. venerupis DOK2-8, which possesses several virulence-related genes. This strain may be potentially virulent to other marine organisms, and its genomic information will provide important insights into the biodiversity of the genus Lacinutrix.

GENOME ANNOUNCEMENT

The genus Lacinutrix, which is a member of the family Flavobacteriaceae (Proteobacteria: Gammaproteobacteria) was created in 2005 and comprises 10 valid marine species, including L. algicola, L. cladophorae, L. copepodicola, L. gracilariae, L. himadriensis, L. iliipiscaria, L. jangbogonensis, L. mariniflava, L. undariae, and L. venerupis (1, 2). Although all of these species were considered nonpathogenic (2), L. venerupis was recently found to be associated with disease outbreak among marine fish (3). Four draft genomes (L. algicola, L. himadriensis, L. jangbogonensis, and L. mariniflava) are currently available in the GenBank database; however, the genome of L. venerupis has not yet been sequenced. Since 2015, we have screened several indigenous bacterial strains with advantageous characteristics for biotechnological applications. Here, we present the first complete genome sequence of an L. venerupis strain isolated from the Republic of Korea.

The DOK2-8 strain was isolated from marine sediment collected from Dokdo, East Sea, Republic of Korea (37°14′25.9″N 131°52′02.6″E), using the standard dilution plating technique on marine agar 2216 (Difco) followed by incubation at 28°C. The 16S rRNA of the isolate (GenBank accession number MG493235) showed >99.9% similarity to L. venerupis Cmf 20.8^T (HG970752); hence, it was finally classified as L. venerupis DOK2-8. The isolate showed strong extracellular proteolytic activity, as determined with the method of Amoozegar et al. (4). Genomic DNA of DOK2-8 was extracted and sequenced at Macrogen, Inc. (Seoul, Republic of Korea), with a PacBio RS II system (Pacific Biosciences) by constructing a 20-kb SMRTbell template library. The PacBio long-read data (1,055,787,767 bp, 122,792 reads) were assembled de novo with the Hierarchical Genome Assembly Process (HGAP) version 3.0 and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/books/NBK174280).

The final assembled circular chromosome of DOK2-8 comprised 3,192,399 bp, with a 30.6% G+C content (92.5% coding region percentage), and encoded 2,857 genes, 2,811 coding sequences, 6 rRNAs (5S, 16S, and 23S), 36 tRNAs, and 4 noncoding RNAs. Overall genome similarities among DOK2-8 and the other four Lacinutrix species strains were assessed using the orthologous average nucleotide identity algorithm (5). The highest genome similarity (80.7%) was with L. algicola (GenBank accession number LIQH00000000), and the lowest (75.5%) was with L. himadriensis (LIQI00000000).

Potential virulence genes in DOK2-8 were identified by searching the Virulence Factor Database (6, 7); consequently, several putative genes involved in capsule biosynthesis, metalloprotease, and htpB chaperonin, which were homologous to those of other Gram-negative species, were detected. Moreover, three putative hemolysin genes were detected in the DOK2-8 genome. These results indicate that L. venerupis DOK2-8 may have potential virulence to other marine organisms, similar to other species in the family Flavobacteriaceae (2), and information regarding its genome will provide important insights into the biodiversity of the genus Lacinutrix in the marine niche. To our knowledge, this is the first study to reveal a complete genome sequence in the genus Lacinutrix.

Accession number(s).

L. venerupis DOK2-8 was deposited in the Korean Agricultural Culture Collection (KACC) as KACC 19202. The 16S rRNA and complete genome (chromosome) of L. venerupis DOK2-8 have been deposited at DDBJ/ENA/GenBank under the accession numbers MG493235 and CP019352, respectively.