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A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome

View ORCID ProfilePoonam Chitale, Alexander D. Lemenze, Emily C. Fogarty, Avi Shah, Courtney Grady, Aubrey R. Odom-Mabey, W. Evan Johnson, Jason H. Yang, A. Murat Eren, Roland Brosch, Pradeep Kumar, David Alland
doi: https://doi.org/10.1101/2022.07.15.500236
Poonam Chitale
1Division of Infectious Disease, Department of Medicine and the Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, and Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
2Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
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  • ORCID record for Poonam Chitale
Alexander D. Lemenze
3Department of Pathology, Immunology and Laboratory Medicine, New Jersey Medical School, Rutgers—The State University of New Jersey, Newark, NJ, USA
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Emily C. Fogarty
4Department of Medicine, University of Chicago, Chicago, IL, USA
5Committee on Microbiology, University of Chicago, Chicago, IL, USA
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Avi Shah
1Division of Infectious Disease, Department of Medicine and the Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, and Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
6Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University- New Jersey Medical School, Newark, New Jersey, USA
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Courtney Grady
1Division of Infectious Disease, Department of Medicine and the Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, and Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
2Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
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Aubrey R. Odom-Mabey
8Division of Computational Biomedicine, Boston University School of Medicine and Bioinformatics Program, Boston University, Boston, MA, USA
9Bioinformatics Program, Boston University, Boston, MA, USA
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W. Evan Johnson
8Division of Computational Biomedicine, Boston University School of Medicine and Bioinformatics Program, Boston University, Boston, MA, USA
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Jason H. Yang
1Division of Infectious Disease, Department of Medicine and the Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, and Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
6Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University- New Jersey Medical School, Newark, New Jersey, USA
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A. Murat Eren
4Department of Medicine, University of Chicago, Chicago, IL, USA
5Committee on Microbiology, University of Chicago, Chicago, IL, USA
7Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
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Roland Brosch
10Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris, 75015, France
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Pradeep Kumar
1Division of Infectious Disease, Department of Medicine and the Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, and Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
2Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
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David Alland
1Division of Infectious Disease, Department of Medicine and the Ray V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, and Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
2Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
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  • For correspondence: allandda@njms.rutgers.edu
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Abstract

H37Rv is the most widely used M. tuberculosis strain. Its genome is globally used as the M. tuberculosis reference sequence. We developed Bact-Builder, a pipeline that leverages consensus building to generate complete and highly accurate gap-closed bacterial genomes and applied it to three independently sequenced cultures of a parental H37Rv laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies were 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contained approximately 6.4 kb additional base pairs encoding ten new regions. These regions included insertions in PE/PPE genes and new paralogs of esxN and esxJ, which were differentially expressed compared to the reference genes. Additional sequencing and assembly with Bact-Builder confirmed that all 10 regions were also present in widely accepted strains of H37Rv: NR123 and TMC102. Bact-builder shows promise as an improved method to perform extremely accurate and reproducible de novo assemblies of bacterial genomes. Furthermore, our findings provide important updates to the primary tuberculosis reference genome.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 16, 2022.
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A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
Poonam Chitale, Alexander D. Lemenze, Emily C. Fogarty, Avi Shah, Courtney Grady, Aubrey R. Odom-Mabey, W. Evan Johnson, Jason H. Yang, A. Murat Eren, Roland Brosch, Pradeep Kumar, David Alland
bioRxiv 2022.07.15.500236; doi: https://doi.org/10.1101/2022.07.15.500236
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A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
Poonam Chitale, Alexander D. Lemenze, Emily C. Fogarty, Avi Shah, Courtney Grady, Aubrey R. Odom-Mabey, W. Evan Johnson, Jason H. Yang, A. Murat Eren, Roland Brosch, Pradeep Kumar, David Alland
bioRxiv 2022.07.15.500236; doi: https://doi.org/10.1101/2022.07.15.500236

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