Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions.
Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions.
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DOI：
10.1038/s41598-020-73562-7
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发表时间：
2020-10-07
影响因子：
4.6
通讯作者：
Rayner JC
中科院分区：
文献类型：
--
作者：
Siegel SV;Chappell L;Hostetler JB;Amaratunga C;Suon S;Böhme U;Berriman M;Fairhurst RM;Rayner JC
由于缺乏强有力的体外培养方法，外周循环中寄生虫密度低，以及寄生虫发育不同步，间日疟原虫基因调控仍然很难研究。我们采用了RNA-seq协议“daft-seq”对四个间日疟原虫田间分离株的转录组进行了测序，这些分离株在体外培养了一段时间后，使用密度梯度进行裂殖体的浓缩。尽管是富含裂殖体的样本，但从PvP01参考基因组的78%中检测到转录。这些广泛的数据被用来确定数千个5‘和3’非翻译区，其中一些与邻近的转录本重叠，并用于改进352个基因的基因模型，包括识别20个新的基因转录本。这一数据集还显著增加了间日疟原虫裂殖体转录本之间的已知异质性。在这些分离株之间发现的差异表达的基因中，大多数缺乏恶性疟原虫的同源基因，并被预测参与宿主与寄生虫的相互作用，富含网织红细胞结合蛋白、裂殖子表面蛋白和功能未知的输出蛋白。更好地理解间日疟原虫转录本中的多样性对于确定新疫苗靶标的优先顺序至关重要。
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.
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影响因子：
64.8
作者：
Carlton, Jane M.;Adams, John H.;Silva, Joana C.;Bidwell, Shelby L.;Lorenzi, Hernan;Caler, Elisabet;Crabtree, Jonathan;Angiuoli, Samuel V.;Merino, Emilio F.;Amedeo, Paolo;Cheng, Qin;Coulson, Richard M. R.;Crabb, Brendan S.;del Portillo, Hernando A.;Essien, Kobby;Feldblyum, Tamara V.;Fernandez-Becerra, Carmen;Gilson, Paul R.;Gueye, Amy H.;Guo, Xiang;Kang'a, Simon;Kooij, Taco W. A.;Korsinczky, Michael;Meyer, Esmeralda V. -S.;Nene, Vish;Paulsen, Ian;White, Owen;Ralph, Stuart A.;Ren, Qinghu;Sargeant, Tobias J.;Salzberg, Steven L.;Stoeckert, Christian J.;Sullivan, Steven A.;Yamamoto, Marcio M.;Hoffman, Stephen L.;Wortman, Jennifer R.;Gardner, Malcolm J.;Galinski, Mary R.;Barnwell, John W.;Fraser-Liggett, Claire M.
通讯作者：
Fraser-Liggett, Claire M.
DOI：
10.1073/pnas.1818485116
发表时间：
2019-04-02
影响因子：
11.1
作者：
Gunalan, Karthigayan;Sa, Juliana M.;Miller, Louis H.
通讯作者：
Miller, Louis H.
影响因子：
14.9
作者：
Ruiz JL;Tena JJ;Bancells C;Cortés A;Gómez-Skarmeta JL;Gómez-Díaz E
通讯作者：
Gómez-Díaz E
影响因子：
9.5
作者：
Carver, Tim;Harris, Simon R.;McQuillan, Jacqueline A.
通讯作者：
McQuillan, Jacqueline A.
影响因子：
14.9
作者：
Balaji S;Babu MM;Iyer LM;Aravind L
通讯作者：
Aravind L