Draft Whole-Genome Sequences of Chryseobacterium piscicola and Chryseobacterium shigense.

We report the draft whole-genome sequences for Chryseobacterium piscicola and Chryseobacterium shigense type strains, bacteria that have been associated with fish gill disease.

GENOME ANNOUNCEMENT

Gill disease is an important disease of cultured fish worldwide. We sequenced the Chryseobacterium species in this report based on their prior association with fish and gill disease (1–4). The purpose is to facilitate investigation of the etiologic agents of gill disease in the United States.

Chryseobacterium spp. type strains were obtained from the Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures (DSM). DNA was extracted using a MO BIO Ultra Clean microbial DNA isolation kit (MO BIO Laboratories, Inc., Carlsbad, CA, USA) according to the manufacturer’s recommendations. Whole-genome sequencing (WGS) was performed using v3 chemistry with paired-end 2× 300-bp reads on the MiSeq platform (Illumina, San Diego, CA, USA). Sequencing libraries were prepared according to the Illumina Nextera XT sample preparation guide.

WGS data were imported into CLC Genomics Workbench, and a de novo assembly was performed using default CLC Genomics Workbench version 8.0 assembly parameters (Qiagen, Valencia, CA, USA). Contigs of less than 300 bp were removed from analysis. The genomes were annotated using the NCBI Prokaryotic Genomes Annotation Pipeline (PGAP V4) (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/). WGS assembly data are shown in Table 1.

TABLE 1

Summary of analyses of type strains associated with fish gill disease

Sample no.	Strain	Species	No. of contigs	Assembly size (bp)	G+C content (%)	Coverage (×)	Total no. of genes	Total no. of CDSa	No. of coding CDS	No. of RNA genes	GenBank accession no.
CVM 43419	DSM 21068	Chryseobacterium piscicola	43	3,444,097	33.82	118	3,110	3,059	3,025	51	MUGO00000000
CVM 43418	DSM 17126	Chryseobacterium shigense	42	4,895,125	37.47	81	4,424	4,353	4,309	71	MUGP00000000

CDS, coding DNA sequences.

The publicly available resistance gene database ResFinder was used for identification of antimicrobial resistance genes, with a 90% sequence identity and 60% length minimum used to identify resistance genes (5). None of the sequenced isolates carried acquired resistance genes.

Accession number(s).

These draft genomes have been deposited in GenBank under the accession no. indicated in Table 1.