{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T08:35:21Z","timestamp":1793694921445,"version":"4.5.1"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T00:00:00Z","timestamp":1738886400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T00:00:00Z","timestamp":1738886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"name":"King Abdullah University of Science and Technology, Saudi Arabia","award":["BAS\/1\/1020-01-01"],"award-info":[{"award-number":["BAS\/1\/1020-01-01"]}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"crossref","award":["82320108014"],"award-info":[{"award-number":["82320108014"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"crossref","award":["82320108014"],"award-info":[{"award-number":["82320108014"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"crossref","award":["82320108014"],"award-info":[{"award-number":["82320108014"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81971967"],"award-info":[{"award-number":["81971967"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82372275"],"award-info":[{"award-number":["82372275"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81971967"],"award-info":[{"award-number":["81971967"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"DOI":"10.1186\/s12864-025-11292-8","type":"journal-article","created":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T07:14:01Z","timestamp":1738912441000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Leveraging genomic insights from the neglected malaria parasites P. malariae and P. ovale using selective whole genome amplification (SWGA) approach"],"prefix":"10.1186","volume":"26","author":[{"given":"Fathia","family":"Ben-Rached","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit Kumar","family":"Subudhi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariah","family":"Alawi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohit","family":"Satyam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sui","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoding","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raeece","family":"Naeem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Mfarrej","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Di","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zenaida","family":"Stead","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Askonas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaobao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Cao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnab","family":"Pain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,2,7]]},"reference":[{"issue":"1","key":"11292_CR1","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1186\/s13071-021-04797-0","volume":"14","author":"J Hawadak","year":"2021","unstructured":"Hawadak J, Dongang Nana RR, Singh V. Global trend of Plasmodium malariae and Plasmodium ovale spp. malaria infections in the last two decades (2000\u20132020): a systematic review and meta-analysis. Parasit Vectors. 2021;14(1):297.","journal-title":"Parasit Vectors"},{"issue":"1","key":"11292_CR2","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1186\/s12936-019-2806-y","volume":"18","author":"R Grande","year":"2019","unstructured":"Grande R, Antinori S, Meroni L, Menegon M, Severini C. A case of Plasmodium malariae recurrence: recrudescence or reinfection? Malar J. 2019;18(1):169.","journal-title":"Malar J"},{"issue":"6","key":"11292_CR3","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1016\/j.pt.2007.04.009","volume":"23","author":"I Mueller","year":"2007","unstructured":"Mueller I, Zimmerman PA, Reeder JC. Plasmodium malariae and Plasmodium ovale\u2013the bashful malaria parasites. Trends Parasitol. 2007;23(6):278\u201383.","journal-title":"Trends Parasitol"},{"issue":"4","key":"11292_CR4","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1128\/CMR.00027-07","volume":"20","author":"WE Collins","year":"2007","unstructured":"Collins WE, Jeffery GM. Plasmodium malariae: parasite and disease. Clin Microbiol Rev. 2007;20(4):579\u201392.","journal-title":"Clin Microbiol Rev"},{"issue":"2","key":"11292_CR5","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1086\/315729","volume":"182","author":"AA Tobian","year":"2000","unstructured":"Tobian AA, Mehlotra RK, Malhotra I, Wamachi A, Mungai P, Koech D, et al. Frequent umbilical cord-blood and maternal-blood infections with Plasmodium Falciparum, P. Malariae, and P. Ovale in Kenya. J Infect Dis. 2000;182(2):558\u201363.","journal-title":"J Infect Dis"},{"issue":"3","key":"11292_CR6","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1128\/CMR.18.3.570-581.2005","volume":"18","author":"WE Collins","year":"2005","unstructured":"Collins WE, Jeffery GM. Plasmodium Ovale: parasite and disease. Clin Microbiol Rev. 2005;18(3):570\u201381.","journal-title":"Clin Microbiol Rev"},{"key":"11292_CR7","doi-asserted-by":"crossref","unstructured":"Hawadak J, Dongang Nana RR, Singh V. Epidemiological, physiological and diagnostic comparison of Plasmodium Ovale Curtisi and Plasmodium Ovale Wallikeri. Diagnostics (Basel). 2021;11(10).","DOI":"10.3390\/diagnostics11101900"},{"issue":"10","key":"11292_CR8","doi-asserted-by":"publisher","first-page":"1544","DOI":"10.1086\/652240","volume":"201","author":"CJ Sutherland","year":"2010","unstructured":"Sutherland CJ, Tanomsing N, Nolder D, Oguike M, Jennison C, Pukrittayakamee S, et al. Two nonrecombining sympatric forms of the human malaria parasite Plasmodium Ovale occur globally. J Infect Dis. 2010;201(10):1544\u201350.","journal-title":"J Infect Dis"},{"key":"11292_CR9","doi-asserted-by":"crossref","unstructured":"Snounou G, Sharp PM, Culleton R. The two parasite species formerly known as Plasmodium Ovale. Trends Parasitol. 2023.","DOI":"10.1016\/j.pt.2023.11.004"},{"issue":"2","key":"11292_CR10","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1128\/JCM.02760-13","volume":"52","author":"HP Fuehrer","year":"2014","unstructured":"Fuehrer HP, Noedl H. Recent advances in detection of Plasmodium Ovale: implications of separation into the two species Plasmodium Ovale Wallikeri and Plasmodium Ovale Curtisi. J Clin Microbiol. 2014;52(2):387\u201391.","journal-title":"J Clin Microbiol"},{"issue":"5","key":"11292_CR11","doi-asserted-by":"publisher","first-page":"e0007414","DOI":"10.1371\/journal.pntd.0007414","volume":"13","author":"V Yman","year":"2019","unstructured":"Yman V, Wandell G, Mutemi DD, Miglar A, Asghar M, Hammar U, et al. Persistent transmission of Plasmodium malariae and Plasmodium ovale species in an area of declining Plasmodium Falciparum transmission in eastern Tanzania. PLoS Negl Trop Dis. 2019;13(5):e0007414.","journal-title":"PLoS Negl Trop Dis"},{"key":"11292_CR12","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1186\/s12936-016-1504-2","volume":"15","author":"Y Cao","year":"2016","unstructured":"Cao Y, Wang W, Liu Y, Cotter C, Zhou H, Zhu G, et al. The increasing importance of Plasmodium Ovale and Plasmodium malariae in a malaria elimination setting: an observational study of imported cases in Jiangsu Province, China, 2011\u20132014. Malar J. 2016;15:459.","journal-title":"Malar J"},{"key":"11292_CR13","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1186\/1475-2875-13-240","volume":"13","author":"C Doderer-Lang","year":"2014","unstructured":"Doderer-Lang C, Atchade PS, Meckert L, Haar E, Perrotey S, Filisetti D, et al. The ears of the African elephant: unexpected high seroprevalence of Plasmodium Ovale and Plasmodium malariae in healthy populations in Western Africa. Malar J. 2014;13:240.","journal-title":"Malar J"},{"issue":"7407","key":"11292_CR14","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1038\/nature11174","volume":"487","author":"M Manske","year":"2012","unstructured":"Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. 2012;487(7407):375\u20139.","journal-title":"Nature"},{"issue":"7214","key":"11292_CR15","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/nature07327","volume":"455","author":"JM Carlton","year":"2008","unstructured":"Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, et al. Comparative genomics of the neglected human malaria parasite Plasmodium Vivax. Nature. 2008;455(7214):757\u201363.","journal-title":"Nature"},{"issue":"3 Suppl","key":"11292_CR16","doi-asserted-by":"publisher","first-page":"87","DOI":"10.4269\/ajtmh.15-0049","volume":"93","author":"JM Carlton","year":"2015","unstructured":"Carlton JM, Volkman SK, Uplekar S, Hupalo DN, Pereira Alves JM, Cui L, et al. Population Genetics, Evolutionary Genomics, and genome-wide studies of Malaria: a View across the International Centers of Excellence for Malaria Research. Am J Trop Med Hyg. 2015;93(3 Suppl):87\u201398.","journal-title":"Am J Trop Med Hyg"},{"issue":"4","key":"11292_CR17","doi-asserted-by":"publisher","first-page":"e0121303","DOI":"10.1371\/journal.pone.0121303","volume":"10","author":"MM Pinheiro","year":"2015","unstructured":"Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD, Lu WC, et al. Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLoS ONE. 2015;10(4):e0121303.","journal-title":"PLoS ONE"},{"issue":"6","key":"11292_CR18","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1038\/ng.2624","volume":"45","author":"O Miotto","year":"2013","unstructured":"Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, et al. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet. 2013;45(6):648\u201355.","journal-title":"Nat Genet"},{"issue":"8","key":"11292_CR19","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1021\/acsinfecdis.5b00049","volume":"1","author":"EL Flannery","year":"2015","unstructured":"Flannery EL, Wang T, Akbari A, Corey VC, Gunawan F, Bright AT, et al. Next-generation sequencing of Plasmodium Vivax patient samples shows evidence of direct evolution in drug-resistance genes. ACS Infect Dis. 2015;1(8):367\u201379.","journal-title":"ACS Infect Dis"},{"issue":"42","key":"11292_CR20","doi-asserted-by":"publisher","first-page":"13027","DOI":"10.1073\/pnas.1509534112","volume":"112","author":"S Assefa","year":"2015","unstructured":"Assefa S, Lim C, Preston MD, Duffy CW, Nair MB, Adroub SA, et al. Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium Knowlesi. Proc Natl Acad Sci U S A. 2015;112(42):13027\u201332.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"11292_CR21","doi-asserted-by":"publisher","first-page":"e0177134","DOI":"10.1371\/journal.pone.0177134","volume":"12","author":"E Diez Benavente","year":"2017","unstructured":"Diez Benavente E, Ward Z, Chan W, Mohareb FR, Sutherland CJ, Roper C, et al. Genomic variation in Plasmodium Vivax malaria reveals regions under selective pressure. PLoS ONE. 2017;12(5):e0177134.","journal-title":"PLoS ONE"},{"issue":"2","key":"11292_CR22","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1534\/genetics.114.165498","volume":"198","author":"AR Leichty","year":"2014","unstructured":"Leichty AR, Brisson D. Selective whole genome amplification for resequencing target microbial species from complex natural samples. Genetics. 2014;198(2):473\u201381.","journal-title":"Genetics"},{"issue":"14","key":"11292_CR23","doi-asserted-by":"publisher","first-page":"2071","DOI":"10.1093\/bioinformatics\/btx118","volume":"33","author":"EL Clarke","year":"2017","unstructured":"Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D. Swga: a primer design toolkit for selective whole genome amplification. Bioinformatics. 2017;33(14):2071\u20137.","journal-title":"Bioinformatics"},{"key":"11292_CR24","doi-asserted-by":"publisher","first-page":"11078","DOI":"10.1038\/ncomms11078","volume":"7","author":"SA Sundararaman","year":"2016","unstructured":"Sundararaman SA, Plenderleith LJ, Liu W, Loy DE, Learn GH, Li Y, et al. Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat Commun. 2016;7:11078.","journal-title":"Nat Commun"},{"issue":"1","key":"11292_CR25","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/s12936-019-2850-7","volume":"18","author":"E Aninagyei","year":"2019","unstructured":"Aninagyei E, Smith-Graham S, Boye A, Egyir-Yawson A, Acheampong DO. Evaluating 18s-rRNA LAMP and selective whole genome amplification (sWGA) assay in detecting asymptomatic Plasmodium falciparum infections in blood donors. Malar J. 2019;18(1):214.","journal-title":"Malar J"},{"key":"11292_CR26","doi-asserted-by":"crossref","unstructured":"Cowell AN, Loy DE, Sundararaman SA, Valdivia H, Fisch K, Lescano AG et al. Selective whole-genome amplification is a robust method that enables scalable whole-genome sequencing of Plasmodium Vivax from Unprocessed Clinical samples. MBio. 2017;8(1).","DOI":"10.1128\/mBio.02257-16"},{"issue":"1","key":"11292_CR27","doi-asserted-by":"publisher","first-page":"9873","DOI":"10.1038\/s41598-019-46398-z","volume":"9","author":"ED Benavente","year":"2019","unstructured":"Benavente ED, Gomes AR, De Silva JR, Grigg M, Walker H, Barber BE, et al. Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations. Sci Rep. 2019;9(1):9873.","journal-title":"Sci Rep"},{"issue":"1","key":"11292_CR28","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1186\/s12936-016-1641-7","volume":"15","author":"SO Oyola","year":"2016","unstructured":"Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, et al. Whole genome sequencing of Plasmodium Falciparum from dried blood spots using selective whole genome amplification. Malar J. 2016;15(1):597.","journal-title":"Malar J"},{"issue":"1","key":"11292_CR29","doi-asserted-by":"publisher","first-page":"10832","DOI":"10.1038\/s41598-020-67568-4","volume":"10","author":"A Ibrahim","year":"2020","unstructured":"Ibrahim A, Diez Benavente E, Nolder D, Proux S, Higgins M, Muwanguzi J, et al. Selective whole genome amplification of Plasmodium malariae DNA from clinical samples reveals insights into population structure. Sci Rep. 2020;10(1):10832.","journal-title":"Sci Rep"},{"issue":"5","key":"11292_CR30","doi-asserted-by":"publisher","first-page":"e0072622","DOI":"10.1128\/spectrum.00726-22","volume":"10","author":"V Joste","year":"2022","unstructured":"Joste V, Guillochon E, Clain J, Coppee R, Houze S. Development and optimization of a selective whole-genome amplification to study Plasmodium Ovale Spp. Microbiol Spectr. 2022;10(5):e0072622.","journal-title":"Microbiol Spectr"},{"issue":"1","key":"11292_CR31","doi-asserted-by":"publisher","first-page":"3843","DOI":"10.1038\/s41598-024-54382-5","volume":"14","author":"M Higgins","year":"2024","unstructured":"Higgins M, Manko E, Ward D, Phelan JE, Nolder D, Sutherland CJ, et al. New reference genomes to distinguish the sympatric malaria parasites, Plasmodium Ovale Curtisi and Plasmodium Ovale Wallikeri. Sci Rep. 2024;14(1):3843.","journal-title":"Sci Rep"},{"issue":"2","key":"11292_CR32","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.ijpddr.2017.03.001","volume":"7","author":"AR Gomes","year":"2017","unstructured":"Gomes AR, Ravenhall M, Benavente ED, Talman A, Sutherland C, Roper C, et al. Genetic diversity of next generation antimalarial targets: a baseline for drug resistance surveillance programmes. Int J Parasitol Drugs Drug Resist. 2017;7(2):174\u201380.","journal-title":"Int J Parasitol Drugs Drug Resist"},{"issue":"11","key":"11292_CR33","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/j.ijpara.2016.05.009","volume":"46","author":"HR Ansari","year":"2016","unstructured":"Ansari HR, Templeton TJ, Subudhi AK, Ramaprasad A, Tang J, Lu F, et al. Genome-scale comparison of expanded gene families in Plasmodium Ovale Wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species. Int J Parasitol. 2016;46(11):685\u201396.","journal-title":"Int J Parasitol"},{"issue":"7639","key":"11292_CR34","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nature21038","volume":"542","author":"GG Rutledge","year":"2017","unstructured":"Rutledge GG, B\u00f6hme U, Sanders M, Reid AJ, Cotton JA, Maiga-Ascofare O, et al. Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature. 2017;542(7639):101.","journal-title":"Nature"},{"key":"11292_CR35","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1002\/0471250953.bi1110s43","volume":"43","author":"GA Van der Auwera","year":"2013","unstructured":"Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinf. 2013;43:1101\u201333.","journal-title":"Curr Protoc Bioinf"},{"issue":"9","key":"11292_CR36","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297\u2013303.","journal-title":"Genome Res"},{"issue":"1","key":"11292_CR37","doi-asserted-by":"publisher","first-page":"10779","DOI":"10.1038\/s41467-024-55102-3","volume":"15","author":"A Ibrahim","year":"2024","unstructured":"Ibrahim A, Mohring F, Manko E, van Schalkwyk DA, Phelan JE, Nolder D, et al. Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility. Nat Commun. 2024;15(1):10779.","journal-title":"Nat Commun"},{"issue":"3","key":"11292_CR38","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1128\/AAC.01200-06","volume":"51","author":"MT Alam","year":"2007","unstructured":"Alam MT, Bora H, Bharti PK, Saifi MA, Das MK, Dev V, et al. Similar trends of pyrimethamine resistance-associated mutations in Plasmodium Vivax and P. Falciparum. Antimicrob Agents Chemother. 2007;51(3):857\u201363.","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"11292_CR39","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1086\/504687","volume":"194","author":"AM McCollum","year":"2006","unstructured":"McCollum AM, Poe AC, Hamel M, Huber C, Zhou Z, Shi YP, et al. Antifolate resistance in Plasmodium Falciparum: multiple origins and identification of novel dhfr alleles. J Infect Dis. 2006;194(2):189\u201397.","journal-title":"J Infect Dis"},{"issue":"4","key":"11292_CR40","doi-asserted-by":"publisher","first-page":"617","DOI":"10.4269\/ajtmh.2006.75.617","volume":"75","author":"A Auliff","year":"2006","unstructured":"Auliff A, Wilson DW, Russell B, Gao Q, Chen N, le Anh N, et al. Amino acid mutations in Plasmodium Vivax DHFR and DHPS from several geographical regions and susceptibility to antifolate drugs. Am J Trop Med Hyg. 2006;75(4):617\u201321.","journal-title":"Am J Trop Med Hyg"},{"issue":"10","key":"11292_CR41","doi-asserted-by":"publisher","first-page":"3523","DOI":"10.1128\/AAC.00234-07","volume":"51","author":"N Tanomsing","year":"2007","unstructured":"Tanomsing N, Imwong M, Pukrittayakamee S, Chotivanich K, Looareesuwan S, Mayxay M, et al. Genetic analysis of the dihydrofolate reductase-thymidylate synthase gene from geographically diverse isolates of Plasmodium malariae. Antimicrob Agents Chemother. 2007;51(10):3523\u201330.","journal-title":"Antimicrob Agents Chemother"},{"issue":"12","key":"11292_CR42","doi-asserted-by":"publisher","first-page":"e0010977","DOI":"10.1371\/journal.pntd.0010977","volume":"16","author":"J Chen","year":"2022","unstructured":"Chen J, Ma X, Tang J, Xu S, Gu Y, Tang F, et al. Disparate selection of mutations in the dihydrofolate reductase gene (dhfr) of Plasmodium Ovale Curtisi and P. o. Wallikeri in Africa. PLoS Negl Trop Dis. 2022;16(12):e0010977.","journal-title":"PLoS Negl Trop Dis"},{"issue":"3","key":"11292_CR43","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1016\/j.parint.2014.09.006","volume":"64","author":"R Isozumi","year":"2015","unstructured":"Isozumi R, Fukui M, Kaneko A, Chan CW, Kawamoto F, Kimura M. Improved detection of malaria cases in island settings of Vanuatu and Kenya by PCR that targets the Plasmodium mitochondrial cytochrome c oxidase III (cox3) gene. Parasitol Int. 2015;64(3):304\u20138.","journal-title":"Parasitol Int"},{"issue":"6","key":"11292_CR44","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software suite. Trends Genet. 2000;16(6):276\u20137.","journal-title":"Trends Genet"},{"key":"11292_CR45","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1111\/j.1467-985X.2010.00676_9.x","volume":"174","author":"C Ginestet","year":"2011","unstructured":"Ginestet C. ggplot2: elegant graphics for data analysis. J Roy Stat Soc A. 2011;174:245.","journal-title":"J Roy Stat Soc A"},{"issue":"15","key":"11292_CR46","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114\u201320.","journal-title":"Bioinformatics"},{"issue":"14","key":"11292_CR47","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"16","key":"11292_CR48","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence Alignment\/Map format and SAMtools. Bioinformatics. 2009;25(16):2078\u20139.","journal-title":"Bioinformatics"},{"key":"11292_CR49","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1002\/0471250953.bi1110s43","volume":"43","author":"GA Van der Auwera","year":"2013","unstructured":"Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinf. 2013;43:11. 0 1\u2009\u2013\u20090 33.","journal-title":"Curr Protoc Bioinf"},{"issue":"15","key":"11292_CR50","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156\u20138.","journal-title":"Bioinformatics"},{"issue":"1","key":"11292_CR51","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24\u20136.","journal-title":"Nat Biotechnol"},{"issue":"W1","key":"11292_CR52","doi-asserted-by":"publisher","first-page":"W256","DOI":"10.1093\/nar\/gkz239","volume":"47","author":"I Letunic","year":"2019","unstructured":"Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"11292_CR53","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094\u2013100.","journal-title":"Bioinformatics"},{"issue":"5","key":"11292_CR54","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722\u201336.","journal-title":"Genome Res"},{"issue":"9","key":"11292_CR55","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","volume":"36","author":"D Guan","year":"2020","unstructured":"Guan D, McCarthy SA, Wood J, Howe K, Wang Y, Durbin R. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896\u20138.","journal-title":"Bioinformatics"},{"issue":"1","key":"11292_CR56","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1186\/s13059-022-02823-7","volume":"23","author":"M Alonge","year":"2022","unstructured":"Alonge M, Lebeigle L, Kirsche M, Jenike K, Ou S, Aganezov S, et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022;23(1):258.","journal-title":"Genome Biol"},{"issue":"9","key":"11292_CR57","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","volume":"19","author":"M Krzywinski","year":"2009","unstructured":"Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639\u201345.","journal-title":"Genome Res"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-025-11292-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-025-11292-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-025-11292-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T07:46:10Z","timestamp":1738914370000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-025-11292-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,7]]},"references-count":57,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["11292"],"URL":"https:\/\/doi.org\/10.1186\/s12864-025-11292-8","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,7]]},"assertion":[{"value":"5 February 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 January 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 February 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The research adhered to the guidelines outlined in the Declaration of Helsinki and informed consent forms were obtained from all patients. All experiments were performed in accordance with the relevant guidelines and regulations and were approved by the Institutional Review Board at KAUST (19IBEC12-Pain) and JIPD (IRB00004221). All data were anonymised before receiving any metadata for analysis. Non-personal identifiers were used during analysis and presentation.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Not applicable.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"118"}}