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Here, a marker was identified and evaluated to genotype <jats:italic>P. falciparum<\/jats:italic> mature gametocytes using amplicon deep sequencing.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A data set of polymorphic regions of the <jats:italic>P. falciparum<\/jats:italic> genome was mined to identify a gametocyte genotyping marker. To assess marker resolution, the number of unique haplotypes in the marker region was estimated from 95 Malawian <jats:italic>P. falciparum<\/jats:italic> whole genome sequences. Specificity of the marker for detection of mature gametocytes was evaluated using reverse transcription-polymerase chain reaction of RNA extracted from NF54 mature gametocytes and rings from a non-gametocyte-producing strain of <jats:italic>P. falciparum<\/jats:italic>. Amplicon deep sequencing was performed on experimental mixtures of mature gametocytes from two distinct parasite clones, as well as gametocyte-positive <jats:italic>P. falciparum<\/jats:italic> field isolates to evaluate the quantitative ability and determine the limit of detection of the genotyping approach.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>A 400\u00a0bp region of the <jats:italic>pfs230<\/jats:italic> gene was identified as a gametocyte genotyping marker. A larger number of unique haplotypes was observed at the <jats:italic>pfs230<\/jats:italic> marker (34) compared to the <jats:italic>sera-2<\/jats:italic> (18) and <jats:italic>ama-1<\/jats:italic> (14) markers in field isolates from Malawi. RNA and DNA genotyping accurately estimated gametocyte and total parasite clone frequencies when evaluating agreement between expected and observed haplotype frequencies in gametocyte mixtures, with concordance correlation coefficients of 0.97 [95% CI: 0.92\u20130.99] and 0.92 [95% CI: 0.83\u20130.97], respectively. The detection limit of the genotyping method for male gametocytes was 0.41 <jats:italic>pfmget<\/jats:italic> transcripts\/\u00b5l [95% CI: 0.28\u20130.72] and for female gametocytes was 1.98 <jats:italic>ccp4<\/jats:italic> transcripts\/\u00b5l [95% CI: 1.35\u20133.68].<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>A region of the <jats:italic>pfs230<\/jats:italic> gene was identified as a marker to genotype <jats:italic>P. falciparum<\/jats:italic> gametocytes. Amplicon deep sequencing of this marker can be used to estimate the number and relative frequency of parasite clones among mature gametocytes within <jats:italic>P. falciparum<\/jats:italic> infections. This gametocyte genotyping marker will be an important tool for studies aimed at understanding dynamics of gametocyte production in polyclonal <jats:italic>P. falciparum<\/jats:italic> infections.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12936-024-04920-3","type":"journal-article","created":{"date-parts":[[2024,4,6]],"date-time":"2024-04-06T16:01:19Z","timestamp":1712419279000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Genotyping Plasmodium falciparum gametocytes using amplicon deep sequencing"],"prefix":"10.1186","volume":"23","author":[{"given":"Jimmy","family":"Vareta","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie A.","family":"Horstman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Adams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karl B.","family":"Seydel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert S.","family":"McCann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren M.","family":"Cohee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam K.","family":"Laufer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shannon","family":"Takala-Harrison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,4,6]]},"reference":[{"key":"4920_CR1","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1128\/CMR.00051-10","volume":"24","author":"T Bousema","year":"2011","unstructured":"Bousema T, Drakeley C. 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