# Complete Genome Sequence of Mycobacterium sp. Strain 4858

Amar Bouam, Anthony Levasseur, Maryline Bonnet, Laurence Borand, Charles van Goethem, Michel Drancourt, Sylvain Godreuil

► To cite this version:

Amar Bouam, Anthony Levasseur, Maryline Bonnet, Laurence Borand, Charles van Goethem, et al. Complete Genome Sequence of Mycobacterium sp. Strain 4858. Microbiology Resource Announcements, 2018, 6 (7), 10.1128/genomeA.01604-17. hal-01970216

HAL Id: hal-01970216

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# Complete Genome Sequence of *Mycobacterium* sp. Strain 4858

Amar Bouam,ª Anthony Levasseur,ª Maryline Bonnet,ᵇ Laurence Borand,ᶜ Charles Van Goethem,ᵈ Michel Drancourt,ª Sylvain Godreuilᵉ

**ABSTRACT** *Mycobacterium* sp. strain 4858 is a nontuberculous mycobacterium isolated from sputum in a Cambodian patient with a pulmonary infection. We report the first complete 5.6-Mbp-long genome sequence of *Mycobacterium* strain 4858, with 68.24% GC content, carrying 5,255 protein-coding genes, 47 tRNAs, and 3 rRNA genes.

*Mycobacterium* sp. strain 4858 is a pigmented slowly growing acid-fast bacillus isolated from a respiratory tract specimen collected from a patient with a pulmonary infection in Cambodia. In order to gain insight into the taxonomic position of this previously undescribed species, we analyzed its whole-genome sequence.

Strain 4858 was cultured on Middlebrook 7H11 agar supplemented with 10% (vol/vol) oleic acid-albumin-dextrose-catalase (Becton, Dickinson, Sparks, MD). The total DNA of strain 4858 was extracted on the EZ1 biorobot (Qiagen) with an EZ1 DNA tissue kit with a 50-µl elution volume. The concentration of extracted DNA measured using the Qubit assay with a high sensitivity kit (Life technologies, Carlsbad, CA, USA) was 55.5 ng/µl. Total DNA was then sequenced using MiSeq technology (Illumina, Inc., San Diego, CA) using the paired-end technique coupled with the mate pair technique. The index representation for strain 4858 was determined to be 5.42%. A total of 683,373 paired-end reads, filtered per the read qualities, were assembled using the SPAdes software (1). The resulting contigs were combined by use of SSPACE (2) assisted by manual finishing and GapFiller (3). This yielded a 5,614,132-bp draft genome with a 68.24% GC content, composed of 8 scaffolds and 12 contigs. Open reading frames (ORFs) were predicted using Prodigal (4) with default parameters. Functional annotation was achieved using BLASTp against the GenBank database (E value, 0.001; coverage, 0.7; identity, 30%) (5) and the Clusters of Orthologous Groups (COG) database (6). When no search results were found, a second round was done against the nonredundant protein sequence (nr) database using BLASTP with an E value of 1 × 10⁻⁰³, coverage of 0.7×, and 30% identity. Noncoding genes and miscellaneous features were predicted using RNAmmer (7), ARAGORN (8), Rfam (9), Pfam (10), and Infernal (11). Of the 5,305 predicted genes, 5,255 were protein-coding genes and 5 were encoded RNAs, including 1 5S rRNA, 1 16S rRNA, 1 23S rRNA, and 47 tRNAs. A total of 4,175 genes (79.45%) were assigned putative functions (by COG or nr BLAST search), 79 genes were identified as ORFans (ORFs with no detected homology to other ORFs in the database) (1.5%), and 831 genes (15.81%) were annotated as hypothetical proteins. The genome of strain 4858 was further analyzed by *in silico* DNA-DNA hybridization (DDH) (12), with genomes exhibiting the closest 16S rRNA gene

**Received** 28 December 2017 **Accepted** 17 January 2018 **Published** 15 February 2018

**Citation** Bouam A, Levasseur A, Bonnet M, Borand L, Van Goethem C, Drancourt M, Godreuil S. 2018. Complete genome sequence of *Mycobacterium* sp. strain 4858. Genome Announc 6:e01604-17. https://doi.org/10.1128/ genomeA.01604-17.

**Copyright** © 2018 Bouam et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Michel Drancourt, Michel.Drancourt@univ-amu.fr.

<footnote>ªHU Méditerranée Infection, MEPHI Aix Marseille Université IRD AP-HM, Marseille, France</footnote>

<footnote>ᵇUMI233-TransVIHMI/INSERM U1175, Institut de Recherche pour le Développement (IRD) and University of Montpellier, Montpellier, France</footnote>

<footnote>ᶜEpidemiology and Public Health, Institut Pasteur du Cambodge, Phom Penh, Cambodia</footnote>

<footnote>ᵈDépartement Biopathologie Cellulaire et Tissulaire des Tumeurs, Centre Hospitalier Universitaire (CHU) de Montpellier, Montpellier, France</footnote>

<footnote>ᵉCentre Hospitalier Universitaire (CHU) de Montpellier, Laboratoire de Bactériologie, MIVEGEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France</footnote>
sequence similarity. The DDH values were estimated using the GGDC (Genome-to-Genome Distance Calculator) version 2.0 online tool (13). This analysis yielded a DDH value of 45% with *Mycobacterium europaeum* CSUR 1344 (GenBank accession number CTEC00000000), 34.50% with *Mycobacterium parascrofulaceum* ATCC BAA-614 (ADNV00000000), 25.60% with *Mycobacterium palustre* DSM 44572 (LQPJ01000000), 23.10% with *Mycobacterium sherrisii* BC1_M4 (MIHC00000000), and *Mycobacterium simiae* ATCC 25275 (CBMJ000000000) and 22.20% with *Mycobacterium kubicae* CIP 106428 (LQPD00000000). These data indicate that *Mycobacterium* sp. strain 4858 is related to the *Mycobacterium simiae* complex of mycobacteria, expanding this large complex to its twentieth species.

**Accession number(s).** The *Mycobacterium* sp. strain 4858 genome sequence has been deposited at EMBL under the accession number OESL01000000.

## REFERENCES

1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455-477. https://doi.org/10.1089/cmb.2012.0021.

2. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578-579. https://doi.org/10.1093/bioinformatics/btq683.

3. Boetzer M, Pirovano W. 2012. Toward almost closed genomes with GapFiller. Genome Biol 13:R56. https://doi.org/10.1186/gb-2012-13-6-r56.

4. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. https://doi.org/10.1186/1471-2105-11-119.

5. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW. 2012. GenBank. Nucleic Acids Res 40:D48-D53. https://doi.org/10.1093/nar/gkr1202.

6. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33-36. https://doi.org/10.1093/nar/28.1.33.

7. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmer: consistent and rapid annotation of ribosomal RNA

genes. Nucleic Acids Res 35:3100-3108. https://doi.org/10.1093/nar/gkm160.

8. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11-16. https://doi.org/10.1093/nar/gkh152.

9. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. 2003. Rfam: an RNA family database. Nucleic Acids Res 31:439-441. https://doi.org/10.1093/nar/gkg006.

10. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucleic Acids Res 40:D290-D301. https://doi.org/10.1093/nar/gkr1065.

11. Nawrocki EP, Kolbe DL, Eddy SR. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25:1335-1337. https://doi.org/10.1093/bioinformatics/btp157.

12. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106: 19126-19131. https://doi.org/10.1073/pnas.0906412106.

13. Auch AF, von Jan M, Klenk HP, Göker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117-134. https://doi.org/10.4056/sigs.531120.