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The unavailability of in vitro culture, and the difficulties in getting a high number of pure parasites makes RNA isolation in quantity and quality a challenge. Here, a methodological outline for RNA-seq from <jats:italic>P. vivax<\/jats:italic> isolates with low parasitemia is presented, combining parasite maturation and enrichment with efficient RNA extraction, yielding\u2009~\u2009100\u00a0pg.\u00b5L<jats:sup>\u22121<\/jats:sup> of RNA, suitable for SMART-Seq Ultra-Low Input RNA library and Illumina sequencing. Unbiased coding transcriptome of\u2009~\u20094\u00a0M reads was achieved for four patient isolates with\u2009~\u200951% of transcripts mapped to the <jats:italic>P. vivax<\/jats:italic> P01 reference genome, presenting heterogeneous profiles of expression among individual isolates. Amongst the most transcribed genes in all isolates, a parasite-staged mixed repertoire of conserved parasite metabolic, membrane and exported proteins was observed. Still, a quarter of transcribed genes remain functionally uncharacterized. In parallel, a <jats:italic>P. falciparum<\/jats:italic> Brazilian isolate was also analyzed and 57% of its transcripts mapped against IT genome. Comparison of transcriptomes of the two species revealed a common trophozoite-staged expression profile, with several homologous genes being expressed. Collectively, these results will positively impact vivax research improving knowledge of <jats:italic>P. vivax<\/jats:italic> biology.<\/jats:p>","DOI":"10.1038\/s41598-021-84607-w","type":"journal-article","created":{"date-parts":[[2021,3,3]],"date-time":"2021-03-03T11:02:36Z","timestamp":1614769356000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax-infected patients"],"prefix":"10.1038","volume":"11","author":[{"given":"Catarina","family":"Bourgard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie C. P.","family":"Lopes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus V. 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