Whole-Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-H4Y, Belonging to INT5 Genotype

Abstract

Here, we report the draft genome sequence of the Mycobacterium intracellulare clinical strain MOTT-H4Y, grouped previously into the INT5 genotype of the 5 genotypes of M. intracellulare.

GENOME ANNOUNCEMENT

Of members of the Mycobacterium avium complex (MAC), Mycobacterium intracellulare has been reported to be isolated more frequently than is M. avium in Korea (1–3). Previously, we reported that the 94 M. intracellulare clinical isolates from Korean patients were divided into 5 genotypes (INT1, INT2, INT3, INT4, and INT5) (4). Recently, we introduced the complete genome sequences of four M. intracellulare strains: two INT2 strains (ATCC 13950^T [GenBank accession no. CP003322] [5] and MOTT-02 [GenBank accession no. CP003323] [6]), one INT1 strain (MOTT-64 [GenBank accession no. CP003324] [7]), and one INT5 strain (MOTT-36Y [GenBank accession no. CP003491] [8]). To understand the phylogenetic and genetic backgrounds of INT5 strains showing phylogenetic distinctness from other M. intracellulare genotypes, whole-genome sequencing of another M. intracellulare INT5 clinical strain, MOTT-H4Y, was performed in this study.

The Mycobacterium sp. MOTT-H4Y genome was sequenced by a standard shotgun strategy using GS FLX pyrosequencing technology. Sequencing analysis was performed in the National Instrumentation Center for Environmental Management (NICEM) (genome analysis unit) at Seoul National University. A total of 787,165 reads were generated, with an average read length of 429, yielding 337,397,625 bp of the total sequences. This represents ~62× coverage for the estimated 5.4 Mb genome size. The assembled sequences contained three contigs (3,099,687 bp, 1,499,525 bp, and 819,111 bp) with a G+C content of 68.09% and a plasmid sequence (24,702 bp) with a G+C content of 65.4%. The obtained contigs were compared for mapping to the whole-genome sequences of the reference strains using the BLASTZ program (http://www.bx.psu.edu/miller_lab/). All the remaining gaps between contigs were completely filled by ~50-fold Solexa reads and PCR amplifications. Genome annotation was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).

A comparison of the Mycobacterium sp. MOTT-H4Y genome with the M. intracellulare ATCC 13950^T and Mycobacterium sp. MOTT-36Y genomes (5, 8) reveals it to have a circular DNA of 5,418,323 bp with a plasmid of 24,702 bp. The genome of Mycobacterium sp. MOTT-H4Y contains similar numbers of protein-coding genes (5,233 open reading frames [ORFs]) as M. intracellulare ATCC 13950^T (5,145 ORFs) and Mycobacterium sp. MOTT-36Y (5,381 ORFs); however, the number of tRNA genes (48 tRNA genes) was greater than those of M. intracellulare ATCC 13950^T (47 tRNA genes) and Mycobacterium sp. MOTT-36Y (46 tRNA genes). The genome of Mycobacterium sp. MOTT-H4Y has a G+C content of 68.09%, and a plasmid was found in its genome with a G+C content of 65.4%. A comparison of predicted ORFs of Mycobacterium sp. MOTT-H4Y with M. intracellulare ATCC 13950^T and Mycobacterium sp. MOTT-36Y showed that they shared 4,685 ORFs (average identity, 95.9%) and 4,988 ORFs (average identity, 98.1%), respectively. Five hundred one ORFs (9.7%) and 547 ORFs (10.5%) were specific to M. intracellulare ATCC 13950^T and Mycobacterium sp. MOTT-H4Y, respectively, and 326 ORFs (6.1%) and 244 ORFs (4.7%) were specific to Mycobacterium sp. MOTT-36Y and Mycobacterium sp. MOTT-H4Y, respectively.

Nucleotide sequence accession number.

Nucleotide sequences of the chromosome and plasmid of Mycobacterium sp. MOTT-H4Y have been deposited in GenBank under the accession no. AKIG00000000.