Complete Genome Sequence of Mycobacterium stephanolepidis.

Mycobacterium stephanolepidis is a rapid-growing nonpigmented species isolated from marine teleost fish (Stephanolepis cirrhifer) and is closely related to Mycobacterium chelonae Here, we report the complete sequence of its genome, comprising a 4.9-Mb chromosome. The sequence represents essential data for future phylogenetic and comparative genome studies of this fish pathogen.

GENOME ANNOUNCEMENT

Mycobacterium stephanolepidis was recently reported by Fukano et al. (1) as a pathogenic agent in thread-sail filefish (Stephanolepis cirrhifer) and black scraper (Thamnaconus modestus) (1, 2). Diseased fish had many white nodules on the surface of the serosae of their internal organs and mesentery (1). The first isolate (NJB0901T) is a reference strain of M. stephanolepidis. Here, we report the complete genome sequence of NJB0901T.

The strain was grown on Middlebrook 7H10 agar medium. DNA was purified with the QIAamp DNA minikit (Qiagen, Hilden, Germany) and NucleoSpin plant II kit (Macherey-Nagel, Düren, Germany). The genome sequence was determined using PacBio reads (14,898 reads, 185,224,950 bases) obtained by the RSII system (Menlo Park, CA, USA) and Illumina 300 × 2 paired-end reads (13,282,712 reads) obtained by a MiSeq sequencer (Illumina, San Diego, CA, USA) (3). The PacBio reads were assembled with Canu version 1.5 (4) into two contigs and circularized using Circlator (5). Alignments produced by mapping Illumina reads to the assembly using the Burrows-Wheeler aligner (6) were used for sequence and assembly error correction with Pilon (7).

The chromosome of NJB0901T is 4,994,485 bp in length, with 64.0% G+C content. The average nucleotide identity was 93.56% between Mycobacterium stephanolepidis and M. chelonae (strain CCUG 47445). The chromosome contains 4,981 predicted protein-coding sequences (CDSs), which is similar to the number of CDSs in M. chelonae strain CCUG 47445 (4,921 CDSs). The genome sequence of M. stephanolepidis NJB0901T represents essential data for future phylogenetic and comparative genome studies of the M. chelonae-M. abscessus group.

Accession number(s).

This complete genome sequence has been deposited at DDBJ/ENA/GenBank under the GenBank accession no. AP018165.