{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:46:40Z","timestamp":1768506400003,"version":"3.49.0"},"posted":{"date-parts":[[2023,5,22]]},"group-title":"Evolutionary Biology","reference-count":82,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,5,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  <jats:italic>Toxoplasma gondii<\/jats:italic>\n                  is a zoonotic protist pathogen that infects up to 1\/3 of the human population. This apicomplexan parasite contains three genome sequences: nuclear (63 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear DNA of mitochondrial origin) and NUPTs (nuclear DNA of plastid origin) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant\n                  <jats:italic>T. gondii<\/jats:italic>\n                  ME49 nuclear genome; the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not\n                  <jats:italic>ku80<\/jats:italic>\n                  mutant,\n                  <jats:italic>Toxoplasma<\/jats:italic>\n                  parasites. Comparisons with\n                  <jats:italic>Neospora caninum<\/jats:italic>\n                  , a species that diverged from\n                  <jats:italic>Toxoplasma<\/jats:italic>\n                  \u223c28 MY ago, revealed that the movement and fixation of 5 NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb) and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Significance Statement<\/jats:title>\n                  <jats:p>\n                    This study reveals how DNA located in cellular compartments called organelles can be transferred to the nucleus of the cell and inserted into the nuclear genome of apicomplexan parasite\n                    <jats:italic>Toxoplasma<\/jats:italic>\n                    . Insertions alter the DNA sequence and may lead to significant changes in how genes function. Unexpectedly, we found that the human protist pathogen,\n                    <jats:italic>Toxoplasma gondii<\/jats:italic>\n                    and closely-related species have the largest observed organellar genome fragment content (&gt;11,000 insertion comprising over 1 Mb of DNA) inserted into their nuclear genome sequence despite their compact 65 Mb nuclear genome. Insertions are occurring at a rate that makes them a significant mutational force that deserves further investigation when examining causes of adaptation and virulence of these parasites.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.05.22.539837","type":"posted-content","created":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T20:35:11Z","timestamp":1684787711000},"source":"Crossref","is-referenced-by-count":1,"title":["Massive invasion of organellar DNA drives nuclear genome evolution in\n                  <i>Toxoplasma<\/i>"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9993-1347","authenticated-orcid":false,"given":"Sivaranjani","family":"Namasivayam","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7476-9224","authenticated-orcid":false,"given":"Cheng","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Assiatu B","family":"Bah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3033-2212","authenticated-orcid":false,"given":"Jenna","family":"Oberstaller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9514-2498","authenticated-orcid":false,"given":"Edwin","family":"Pierre-Louis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9144-287X","authenticated-orcid":false,"given":"Ronald Drew","family":"Etheridge","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8772-6976","authenticated-orcid":false,"given":"Cedric","family":"Feschotte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6548-8348","authenticated-orcid":false,"given":"Ellen J.","family":"Pritham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6413-1101","authenticated-orcid":false,"given":"Jessica C.","family":"Kissinger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023052921050602000_2023.05.22.539837v2.1","doi-asserted-by":"publisher","DOI":"10.1016\/S0020-7519(00)00124-7"},{"key":"2023052921050602000_2023.05.22.539837v2.2","doi-asserted-by":"crossref","unstructured":"J. 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