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Complete Genome Sequence of Mycobacterium shigaense

June 2018
Genome Announcements 6(25)

June 2018
6(25)

DOI:10.1128/genomeA.00552-18

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CC BY 4.0

Authors:

Mitsunori Yoshida

National Institute of Infectious Diseases

Hanako Fukano

National Institute of Infectious Diseases, Tokyo

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Mycobacterium shigaense is a slowly growing schotochromogenic species and a member of Mycobacterium simiae complex group. Here we report the complete sequence of its genome comprising a 5.2-Mb chromosome. The sequence will represent the essential data for future phylogenetic and comparative genome studies of Mycobacterium simiae complex group.

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Complete Genome Sequence of Mycobacterium shigaense

Mitsunori Yoshida,

Hanako Fukano,

Yoshitoshi Ogura,

Yuko Kazumi,

Satoshi Mitarai,

Tetsuya Hayashi,

Yoshihiko Hoshino

Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo,

Japan

Department of Bacteriology, Faculty of Medicine Sciences, Kyushu University, Fukuoka, Japan

The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan

ABSTRACT Mycobacterium shigaense is a slowly growing scotochromogenic species

and a member of the Mycobacterium simiae complex group. Here, we report the

complete sequence of its genome, comprising a 5.2-Mb chromosome. The sequence

will represent the essential data for future phylogenetic and comparative genome

studies of the Mycobacterium simiae complex group.

Mycobacterium shigaense was reported by Nakanaga et al. in 2012 as a causative

agent of skin lesions in an immune-suppressed patient (1). After that, a total of six

patients were diagnosed and another three cases have already been reported, and we

recently summarized the characteristics of M. shigaense (2–5). Notably, among four out

of six patients (66.7%), the place they live is the Shiga prefecture, for which this strain

is named. The ﬁrst clinical isolate (JCM 32072

) is a reference strain of “M. shigaense.”

Here, we report the complete genome sequence of JCM 32072

The strain was grown with Middlebrook 7H9 medium. DNA was puriﬁed with the

standard phenol-chloroform method. The genome sequence was determined using

PacBio reads (149,374 subreads) obtained with an RS II system (Menlo Park, CA, USA),

and Illumina 150 ⫻2 paired-end reads (692,827 reads) obtained with a MiSeq se-

quencer (Illumina, San Diego, USA) were used for correction of sequence and assembly

errors (6–10). The reads were assembled into one contig by using the HGAP/Quiver

assembly approach (11) and circularized using Circlator (12). Alignments produced by

mapping Illumina reads to the assembly using the Burrows–Wheeler aligner (13) were

used for correction of sequence and assembly errors with Pilon (14). Automated

annotation was carried out with the DDBJ Fast Annotation and Submission Tool

(DFAST) (https://dfast.nig.ac.jp)(8, 9, 15, 16). Average nucleotide identity (ANI) was

calculated by JSpeciesWS (17).

The chromosome of JCM 32072

is 5,232,660 bp in length with 67.3% G⫹C content.

The average nucleotide identities for this strain were between 76 and 81% of those for

the M. simiae complex group (3). The chromosome contains 4,920 predicted protein-

coding sequences (CDS), which is much fewer than those of the M. simiae strain MO323

(5,664 CDS). The genome sequence of M. shigaense JCM 32072

will represent the

essential data for future phylogenetic and comparative genome studies and will be

useful for better understanding the evolution of the M. simiae complex group.

Accession number(s). This complete genome sequence has been deposited at

DDBJ/ENA/GenBank under the accession no. AP018164.

ACKNOWLEDGMENTS

This work was supported in part by a grant from the Japan Agency for Medical

Research and Development/Japan International Cooperation Agency (AMED) to Y.

Hoshino (jp18fk0108043, jp18fk0108064, jp18fk0108075, and jp18jm0510004), by a

Grant-in-Aid for Scientiﬁc Research (C) from the Japan Society for the Promotion of

Received 17 May 2018 Accepted 21 May

2018 Published 21 June 2018

Citation Yoshida M, Fukano H, Ogura Y,

Kazumi Y, Mitarai S, Hayashi T, Hoshino Y. 2018.

Complete genome sequence of

Mycobacterium shigaense. Genome Announc

6:e00552-18. https://doi.org/10.1128/genomeA

.00552-18.

open-access article distributed under the terms

of the Creative Commons Attribution 4.0

International license.

Address correspondence to Yoshihiko Hoshino,

yhoshino@nih.go.jp.

PROKARYOTES

crossm

Volume 6 Issue 25 e00552-18 genomea.asm.org 1

Science (JSPS) to Y. Hoshino (jp18K08312), by a Grant-in-Aid for Young Scientists (B) to

M. Yoshida (jp17K16066), and by a Grant-in-Aid for Early-Career Scientists to H. Fukano

(jp18K15966). The funders had no role in study design, data collection and analysis,

decision to publish, or preparation of the manuscript.

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