The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex.
<h4>Background</h4>M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis.<h4>Methodology/principal findings</h4>In search of...
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Neglected Tropical Diseases |
| Online Access: | https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0001552&type=printable |
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| author | Stephen D Bentley Iñaki Comas Josephine M Bryant Danielle Walker Noel H Smith Simon R Harris Scott Thurston Sebastien Gagneux Jonathan Wood Martin Antonio Michael A Quail Florian Gehre Richard A Adegbola Julian Parkhill Bouke C de Jong |
| author_facet | Stephen D Bentley Iñaki Comas Josephine M Bryant Danielle Walker Noel H Smith Simon R Harris Scott Thurston Sebastien Gagneux Jonathan Wood Martin Antonio Michael A Quail Florian Gehre Richard A Adegbola Julian Parkhill Bouke C de Jong |
| author_sort | Stephen D Bentley |
| collection | DOAJ |
| description | <h4>Background</h4>M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis.<h4>Methodology/principal findings</h4>In search of candidate genes underlying these differences, the genome of M. africanum West African 2 was sequenced using classical capillary sequencing techniques. Our findings reveal a unique sequence, RD900, that was independently lost during the evolution of two important lineages within the complex: the "modern" M. tuberculosis group and the lineage leading to M. bovis. Closely related to M. bovis and other animal strains within the M. tuberculosis complex, M. africanum West African 2 shares an abundance of pseudogenes with M. bovis but also with M. africanum West African clade 1. Comparison with other strains of the M. tuberculosis complex revealed pseudogenes events in all the known lineages pointing toward ongoing genome erosion likely due to increased genetic drift and relaxed selection linked to serial transmission-bottlenecks and an intracellular lifestyle.<h4>Conclusions/significance</h4>The genomic differences identified between M. africanum West African 2 and the other strains of the Mycobacterium tuberculosis complex may explain its attenuated phenotype, and pave the way for targeted experiments to elucidate the phenotypic characteristic of M. africanum. Moreover, availability of the whole genome data allows for verification of conservation of targets used for the next generation of diagnostics and vaccines, in order to ensure similar efficacy in West Africa. |
| format | Article |
| id | doaj-art-abf159ae3dd944bc8659b7ee46c00486 |
| institution | OA Journals |
| issn | 1935-2727 1935-2735 |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Neglected Tropical Diseases |
| spelling | doaj-art-abf159ae3dd944bc8659b7ee46c004862025-08-20T02:33:12ZengPublic Library of Science (PLoS)PLoS Neglected Tropical Diseases1935-27271935-27352012-01-0162e155210.1371/journal.pntd.0001552The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex.Stephen D BentleyIñaki ComasJosephine M BryantDanielle WalkerNoel H SmithSimon R HarrisScott ThurstonSebastien GagneuxJonathan WoodMartin AntonioMichael A QuailFlorian GehreRichard A AdegbolaJulian ParkhillBouke C de Jong<h4>Background</h4>M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis.<h4>Methodology/principal findings</h4>In search of candidate genes underlying these differences, the genome of M. africanum West African 2 was sequenced using classical capillary sequencing techniques. Our findings reveal a unique sequence, RD900, that was independently lost during the evolution of two important lineages within the complex: the "modern" M. tuberculosis group and the lineage leading to M. bovis. Closely related to M. bovis and other animal strains within the M. tuberculosis complex, M. africanum West African 2 shares an abundance of pseudogenes with M. bovis but also with M. africanum West African clade 1. Comparison with other strains of the M. tuberculosis complex revealed pseudogenes events in all the known lineages pointing toward ongoing genome erosion likely due to increased genetic drift and relaxed selection linked to serial transmission-bottlenecks and an intracellular lifestyle.<h4>Conclusions/significance</h4>The genomic differences identified between M. africanum West African 2 and the other strains of the Mycobacterium tuberculosis complex may explain its attenuated phenotype, and pave the way for targeted experiments to elucidate the phenotypic characteristic of M. africanum. Moreover, availability of the whole genome data allows for verification of conservation of targets used for the next generation of diagnostics and vaccines, in order to ensure similar efficacy in West Africa.https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0001552&type=printable |
| spellingShingle | Stephen D Bentley Iñaki Comas Josephine M Bryant Danielle Walker Noel H Smith Simon R Harris Scott Thurston Sebastien Gagneux Jonathan Wood Martin Antonio Michael A Quail Florian Gehre Richard A Adegbola Julian Parkhill Bouke C de Jong The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. PLoS Neglected Tropical Diseases |
| title | The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. |
| title_full | The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. |
| title_fullStr | The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. |
| title_full_unstemmed | The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. |
| title_short | The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. |
| title_sort | genome of mycobacterium africanum west african 2 reveals a lineage specific locus and genome erosion common to the m tuberculosis complex |
| url | https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0001552&type=printable |
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