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This is due to limitations in traditional short-read sequencing and linear reference-based analyses, which can miss complex structural changes. Tuberculosis (TB), a disease caused by\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    (\n                    <jats:italic>Mtb<\/jats:italic>\n                    ), remains a major global health concern. In this study, we harness long-read sequencing technologies and genome graph tools to construct a\n                    <jats:italic>Mtb<\/jats:italic>\n                    pangenome reference graph (PRG) from 859 high-quality, diverse, long-read assemblies. To enable accurate genotyping of SVs leveraging the PRG, we developed miniwalk, a tool that outperforms a traditional linear genome-based approach in precision for SV detection. We characterize patterns of structural variation genome-wide, revealing a virulence-associated ESX-5 deletion to be recurrent across the phylogeny, and fixed in a sub-lineage of L4. Systematic screens for additional genes that are recurrently affected by SVs implicated those related to metal homeostasis, including a copper exporter fixed in the widely distributed L1.2.1 sub-lineage. Lastly, we genotyped 41,134 isolates and found SVs putatively associated with resistance to various first and second-line drugs. These findings underscore the broader role of SVs in shaping\n                    <jats:italic>Mtb<\/jats:italic>\n                    diversity, highlighting their importance in both understanding evolution and designing strategies to combat drug-resistant TB.\n                  <\/jats:p>","DOI":"10.1038\/s41467-025-65779-9","type":"journal-article","created":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T15:33:54Z","timestamp":1764344034000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance"],"prefix":"10.1038","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8366-7377","authenticated-orcid":false,"given":"Aleix","family":"Canalda-Baltrons","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1527-5168","authenticated-orcid":false,"given":"Matthew","family":"Silcocks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3683-6208","authenticated-orcid":false,"given":"Michael B.","family":"Hall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derrick","family":"Theys","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7471-4768","authenticated-orcid":false,"given":"Xuling","family":"Chang \u5e38\u620c\u7075","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4174-1142","authenticated-orcid":false,"given":"Linda T.","family":"Viberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7789-8360","authenticated-orcid":false,"given":"Norelle L.","family":"Sherry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4300-455X","authenticated-orcid":false,"given":"Lachlan","family":"Coin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7873-933X","authenticated-orcid":false,"given":"Sarah J.","family":"Dunstan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,28]]},"reference":[{"key":"65779_CR1","unstructured":"WHO. 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