{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:19:02Z","timestamp":1792790342206,"version":"4.5.0"},"posted":{"date-parts":[[2026,2,27]]},"group-title":"Genomics","reference-count":78,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T00:00:00Z","timestamp":1772150400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health","award":["R01AI155765"],"award-info":[{"award-number":["R01AI155765"]}]},{"name":"National Institutes of Health","award":["T15LM007092"],"award-info":[{"award-number":["T15LM007092"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Despite the long-held view of\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  (\n                  <jats:italic>Mtb<\/jats:italic>\n                  ) as a genetically conserved pathogen, many genomic regions remain poorly resolved due to high sequence homology and repetitive content. Using complete genome assemblies generated from long-read sequencing of 151 globally representative clinical isolates, we comprehensively analyzed genome-wide patterns of genetic diversity and evolution across the\n                  <jats:italic>Mtb<\/jats:italic>\n                  genome. Our analysis uncovers pronounced diversity hotspots within paralogous regions generated by recurrent gene conversion between homologous genes. In many cases, these hotspots exhibit more than an order of magnitude greater genetic diversity than the rest of the\n                  <jats:italic>Mtb<\/jats:italic>\n                  genome, which is otherwise characterized by remarkably low variation. Mutations within these regions display clustered substitution patterns, excess paralog-matching variants, and distinct mutational spectra consistent with ongoing gene conversion. Our analysis identifies over 300 individual gene conversion events distributed throughout the\n                  <jats:italic>Mtb<\/jats:italic>\n                  phylogeny. These gene conversion events occur predominantly within gene families associated with virulence and host-pathogen interactions, including the PE, PPE, and ESX families. Several of the most pronounced diversity hotspots occur in antigens encoded within paralogous regions. Among these, the vaccine candidate PPE18 harbors mutations in validated epitope sequences and predicted alterations in HLA-II binding. Together, these findings demonstrate that gene conversion actively shapes antigenic and virulence-associated diversity in\n                  <jats:italic>Mtb<\/jats:italic>\n                  .\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Significance Statement<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    , the bacterium that causes tuberculosis, is widely considered a genetically conserved pathogen. However, repetitive regions comprising nearly 10% of its genome have historically been excluded from genomic analyses. Using complete genome assemblies from diverse clinical isolates, we show that gene conversion, a form of recombination between paralogous genes within the same genome, is a major driver of diversity in these previously unresolved regions. Gene conversion generates pronounced diversity hotspots that are often more than ten times more variable than the genomic background. Many of these hotspots occur in genes involved in virulence and host interaction. Notably, the vaccine antigen PPE18 undergoes recurrent gene conversion, highlighting a mechanism that can shape antigen diversity relevant to tuberculosis vaccine development.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.02.26.708061","type":"posted-content","created":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T00:00:18Z","timestamp":1772236818000},"source":"Crossref","is-referenced-by-count":3,"title":["Gene conversion is a key driver of diversity hotspots in\n                  <i>M. tuberculosis<\/i>\n                  antigens and virulence-associated loci"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9108-3328","authenticated-orcid":false,"given":"Maximillian G.","family":"Marin","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, USA"},{"name":"Department of Data Science, Dana-Farber Cancer Institute, Boston, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4612-6819","authenticated-orcid":false,"given":"Natalia","family":"Quinones-Olvera","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8657-5686","authenticated-orcid":false,"given":"Hu","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8789-0912","authenticated-orcid":false,"given":"Michael A.","family":"Harris","sequence":"additional","affiliation":[{"name":"Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6658-9040","authenticated-orcid":false,"given":"Brendan M.","family":"Jeffrey","sequence":"additional","affiliation":[{"name":"Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4190-9045","authenticated-orcid":false,"given":"Alex","family":"Rosenthal","sequence":"additional","affiliation":[{"name":"Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3677-2876","authenticated-orcid":false,"given":"Kenan C.","family":"Murphy","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6178-4329","authenticated-orcid":false,"given":"Christopher","family":"Sassetti","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4874-2874","authenticated-orcid":false,"given":"Heng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, USA"},{"name":"Department of Data Science, Dana-Farber Cancer Institute, Boston, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3871-5760","authenticated-orcid":false,"given":"Maha R.","family":"Farhat","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, USA"},{"name":"Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092507001490000_2026.02.26.708061v4.1","unstructured":"Global tuberculosis report 2024. 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