{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T16:23:12Z","timestamp":1761582192422,"version":"3.41.2"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T00:00:00Z","timestamp":1652745600000},"content-version":"vor","delay-in-days":47,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"DBT-Genome Engineering Technologies","award":["BT\/PR25858\/GET\/119\/169\/2017"],"award-info":[{"award-number":["BT\/PR25858\/GET\/119\/169\/2017"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-nucleotide variations (SNVs) in RNA, arising from co- and post-transcriptional phenomena including transcription errors and RNA-editing, are well studied in a range of organisms. In the malaria parasite Plasmodium falciparum, stage-specific and non-specific gene-expression variations accompany the parasite's array of developmental and morphological phenotypes over the course of its complex life cycle. However, the extent, rate and effect of sequence-level variation in the parasite's transcriptome are unknown. Here, we report the presence of pervasive, non-specific SNVs in the P. falciparum transcriptome. SNV rates for a gene were correlated to gene length (r$ \\approx$0.65\u20130.7) but not to the AT-content of that gene. Global SNV rates for the P. falciparum lines we used, and for publicly available P. vivax and P. falciparum clinical isolate datasets, were of the order of 10\u20133 per base, \u223c10\u00d7\u00a0higher than rates we calculated for bacterial datasets. These variations may reflect an intrinsic transcriptional error rate in the parasite, and RNA editing may be responsible for a subset of them. This seemingly characteristic property of the parasite may have implications for clinical outcomes and the basic biology and evolution of P. falciparum and parasite biology more broadly. We anticipate that our study will prompt further investigations into the exact sources, consequences and possible adaptive roles of these SNVs.<\/jats:p>","DOI":"10.1093\/nargab\/lqac036","type":"journal-article","created":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T12:26:57Z","timestamp":1652790417000},"source":"Crossref","is-referenced-by-count":4,"title":["Pervasive sequence-level variation in the transcriptome of <i>Plasmodium falciparum<\/i>"],"prefix":"10.1093","volume":"4","author":[{"given":"Bruhad","family":"Dave","sequence":"first","affiliation":[{"name":"Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abhishek","family":"Kanyal","sequence":"additional","affiliation":[{"name":"Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D V","family":"Mamatharani","sequence":"additional","affiliation":[{"name":"Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5714-0587","authenticated-orcid":false,"given":"Krishanpal","family":"Karmodiya","sequence":"additional","affiliation":[{"name":"Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,17]]},"reference":[{"key":"2022051712263796200_B1","doi-asserted-by":"crossref","first-page":"e1000644","DOI":"10.1371\/journal.ppat.1000644","article-title":"Comparative transcriptional and genomic analysis of plasmodium falciparum field isolates","volume":"5","author":"Mackinnon","year":"2009","journal-title":"PLoS Pathog."},{"year":"2020","author":"World Malaria Report","key":"2022051712263796200_B2"},{"key":"2022051712263796200_B3","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1101\/gr.129692.111","article-title":"Transcriptional variation in the malaria parasite plasmodium falciparum","volume":"22","author":"Rovira-Graells","year":"2012","journal-title":"Genome Res."},{"key":"2022051712263796200_B4","doi-asserted-by":"crossref","first-page":"e00008","DOI":"10.1128\/Spectrum.00008-21","article-title":"Single-cell RNA sequencing reveals cellular heterogeneity and stage transition under temperature stress in synchronized plasmodium falciparum cells","volume":"9","author":"Rawat","year":"2021","journal-title":"Microbiol. 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Evol."}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/4\/2\/lqac036\/43733802\/lqac036.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/4\/2\/lqac036\/43733802\/lqac036.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T12:27:27Z","timestamp":1652790447000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqac036\/6586825"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,3,31]]},"references-count":43,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,3,31]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqac036","relation":{},"ISSN":["2631-9268"],"issn-type":[{"type":"electronic","value":"2631-9268"}],"subject":[],"published-other":{"date-parts":[[2022,6,1]]},"published":{"date-parts":[[2022,3,31]]},"article-number":"lqac036"}}