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Here, we present the first comprehensive study of DNA replication origin specification and activation during Plasmodium schizogony. Potential replication origins were abundant, with ORC1-binding sites detected every \u223c800 bp. In this extremely A\/T-biased genome, the sites were biased towards areas of higher G\/C content, and contained no specific sequence motif. Origin activation was then measured at single-molecule resolution using newly developed DNAscent technology: a powerful method of detecting replication fork movement via base analogues in DNA sequenced on the Oxford Nanopore platform. Unusually, origins were preferentially activated in areas of low transcriptional activity, and replication forks also moved fastest through lowly transcribed genes. This contrasts with the way that origin activation is organised in other systems, such as human cells, and suggests that P. falciparum has evolved its S-phase specifically to minimise conflicts between transcription and origin firing. This may be particularly important to maximise the efficiency and accuracy of schizogony, with its multiple rounds of DNA replication and its absence of canonical cell-cycle checkpoints.<\/jats:p>","DOI":"10.1093\/nar\/gkad093","type":"journal-article","created":{"date-parts":[[2023,2,20]],"date-time":"2023-02-20T13:29:27Z","timestamp":1676899767000},"page":"2709-2724","source":"Crossref","is-referenced-by-count":34,"title":["A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite<i>Plasmodium falciparum<\/i>"],"prefix":"10.1093","volume":"51","author":[{"given":"Francis\u00a0Isidore\u00a0Garcia","family":"Tota\u00f1es","sequence":"first","affiliation":[{"name":"Department of Pathology, University of Cambridge , Tennis Court Road , Cambridge \u00a0CB2 1QP, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas","family":"Gockel","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Radboud University , Geert Grooteplein 26-28 , 6525 GA\u00a0 Nijmegen , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah E","family":"Chapman","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cambridge , Tennis Court Road , Cambridge \u00a0CB2 1QP, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8460-6477","authenticated-orcid":false,"given":"Rich\u00e1rd","family":"B\u00e1rtfai","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Radboud University , Geert Grooteplein 26-28 , 6525 GA\u00a0 Nijmegen , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael\u00a0A","family":"Boemo","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cambridge , Tennis Court Road , Cambridge \u00a0CB2 1QP, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7583-2176","authenticated-orcid":false,"given":"Catherine\u00a0J","family":"Merrick","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cambridge , Tennis Court Road , Cambridge \u00a0CB2 1QP, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,2,20]]},"reference":[{"key":"2023041100085218900_","doi-asserted-by":"crossref","first-page":"e204","DOI":"10.1371\/journal.pmed.0020204","article-title":"Estimation of the total parasite biomass in acute Falciparum malaria from plasma PfHRP2","volume":"2","author":"Dondorp","year":"2005","journal-title":"PLoS Med."},{"key":"2023041100085218900_","doi-asserted-by":"crossref","first-page":"42","DOI":"10.4269\/ajtmh.14-0841","article-title":"Investigating the pathogenesis of severe malaria: a multidisciplinary and cross-geographical approach","volume":"93","author":"Wassmer","year":"2015","journal-title":"Am. 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