Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
Sci Rep. 2020 Oct 7;10(1):16667. doi: 10.1038/s41598-020-73562-7.
Plasmodium vivax gene regulation remains difficult to study due to the lack of a robust in vitro culture method, low parasite densities in peripheral circulation and asynchronous parasite development. We adapted an RNA-seq protocol "DAFT-seq" to sequence the transcriptome of four P. vivax field isolates that were cultured for a short period ex vivo before using a density gradient for schizont enrichment. Transcription was detected from 78% of the PvP01 reference genome, despite being schizont-enriched samples. This extensive data was used to define thousands of 5' and 3' untranslated regions, some of which overlapped with neighbouring transcripts, and to improve the gene models of 352 genes, including identifying 20 novel gene transcripts. This dataset has also significantly increased the known amount of heterogeneity between P. vivax schizont transcriptomes from individual patients. The majority of genes found to be differentially expressed between the isolates lack Plasmodium falciparum homologs and are predicted to be involved in host-parasite interactions, with an enrichment in reticulocyte binding proteins, merozoite surface proteins and exported proteins with unknown function. An improved understanding of the diversity within P. vivax transcriptomes will be essential for the prioritisation of novel vaccine targets.
由于缺乏有效的体外培养方法、外周血循环中寄生虫密度低以及寄生虫发育不同步，导致对间日疟原虫基因调控的研究仍然具有挑战性。我们对四种间日疟原虫野外分离株进行了 RNA 测序（RNA-seq）协议“DAFT-seq”的改编，这些分离株在使用密度梯度进行裂殖子富集之前进行了短暂的体外培养。尽管是裂殖子富集样本，但在 78%的 PvP01 参考基因组中检测到转录。该广泛的数据用于定义数千个 5'和 3'非翻译区，其中一些与相邻的转录本重叠，并改进了 352 个基因的基因模型，包括鉴定出 20 个新的基因转录本。该数据集还显著增加了来自单个患者的间日疟原虫裂殖子转录组之间已知的异质性数量。在分离株之间发现的大多数差异表达基因缺乏恶性疟原虫同源物，预计与宿主-寄生虫相互作用有关，富含网织红细胞结合蛋白、裂殖子表面蛋白和具有未知功能的分泌蛋白。对间日疟原虫转录组内多样性的深入了解对于确定新型疫苗靶标至关重要。
