{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T17:08:13Z","timestamp":1778951293314,"version":"3.51.4"},"posted":{"date-parts":[[2026,5,13]]},"group-title":"Cell Biology","reference-count":62,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:00:00Z","timestamp":1778630400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  <jats:italic>Plasmodium vivax<\/jats:italic>\n                  (\n                  <jats:italic>Pv<\/jats:italic>\n                  ) infections are developmentally asynchronous and often polyclonal, complicating interpretation of bulk parasite transcriptomes. Here, we analyzed paired\n                  <jats:italic>in vivo<\/jats:italic>\n                  and short-term\n                  <jats:italic>ex vivo<\/jats:italic>\n                  transcriptomes from Ethiopian clinical isolates using stage deconvolution and\n                  <jats:italic>PvMSP<\/jats:italic>\n                  1 haplotyping.\n                  <jats:italic>Ex vivo<\/jats:italic>\n                  maturation modestly increased inferred schizont representation while largely preserving the proportion of trophozoites and gametocytes. After adjustment for parasite stage composition,\n                  <jats:italic>in vivo<\/jats:italic>\n                  and\n                  <jats:italic>ex vivo<\/jats:italic>\n                  transcriptomes remained globally similar, with no genes significantly differentially expressed, indicating the absence of major culture-induced transcriptional response. In contrast, short-term culture reduced multiplicity of infection, contracted within-host haplotype diversity, and non-randomly depleted specific haplotypes, consistent with a clonal bottleneck. In a subset of low-complexity infections, residual expression patterns were clustered by dominant haplotype, suggesting genotype-associated transcriptional heterogeneity independent of developmental stage. Together, these findings indicate that short-term\n                  <jats:italic>ex vivo<\/jats:italic>\n                  culture enriches late asexual stages and selectively filters clones rather than inducing a common transcriptional program. These results shows that ex vivo cultures are reliable way to study gene expression, especially for late stages. However, these needs explicitly model developmental composition and infection complexity when interpreting\n                  <jats:italic>Pv<\/jats:italic>\n                  transcriptomes from natural infections\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Author summary<\/jats:title>\n                  <jats:p>\n                    Malaria caused by\n                    <jats:italic>Plasmodium vivax<\/jats:italic>\n                    is difficult to study because this parasite cannot yet be grown continuously in the laboratory and infections in patients often contain parasites at different developmental stages and multiple parasite lineages at the same time. In this study, we wanted to understand how much of the parasite gene-expression signal reflects true biological differences, and how much is explained by parasite development or changes that occur during short-term laboratory maturation. We compared parasites collected directly from patients in Ethiopia with matched parasite matured briefly outside the body. We found that short-term culture mainly increased the proportion of later-stage parasites, but after accounting for developmental stage, the overall gene-expression patterns remained very similar. However, culture reduced the diversity of parasite lineages within infections, suggesting that some parasite lineages survive better than others under laboratory conditions. Our findings highlight that natural\n                    <jats:italic>Pv<\/jats:italic>\n                    infections are complex mixtures of parasite stages and lineages. Accounting for this complexity will improve how researchers interpret parasite gene-expression studies and design future studies of parasite invasion, transmission, and survival.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.05.11.724466","type":"posted-content","created":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T07:50:19Z","timestamp":1778745019000},"source":"Crossref","is-referenced-by-count":0,"title":["Stage-aware transcriptomics reveals selective haplotype persistence in short-term\n                  <i>ex vivo<\/i>\n                  cultured\n                  <i>Plasmodium vivax<\/i>"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7205-9496","authenticated-orcid":false,"given":"Beka","family":"Abagero","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA"},{"name":"Tropical and Infectious Diseases 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Health, Jimma University, Jimma, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Tesefay","sequence":"additional","affiliation":[{"name":"School of Medical Laboratory Sciences, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Biniyam","family":"Lukas","sequence":"additional","affiliation":[{"name":"School of Medical Laboratory Sciences, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tassew","family":"Shenkutie","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3135-1175","authenticated-orcid":false,"given":"Jean","family":"Popovici","sequence":"additional","affiliation":[{"name":"Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh Cambodia"},{"name":"Infectious Disease Epidemiology and Analytics G5, Institut Pasteur, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Delenesaw","family":"Yewhalaw","sequence":"additional","affiliation":[{"name":"Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia"},{"name":"School of Medical Laboratory Sciences, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Serre","sequence":"additional","affiliation":[{"name":"Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, 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