Department of Cell Biology, Institute for Childhood and Neglected Diseases 202, The Scripps Research Institute, La Jolla, CA 92037, USA.
Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):20045-50. doi: 10.1073/pnas.1003776107. Epub 2010 Oct 29.
Plasmodium vivax causes 25-40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the P. vivax reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole-genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole-genome sequencing (30× coverage). This analysis revealed over 18,261 single-nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Salvador I strain obtained in 1972. This full-genome sequence of an uncultured P. vivax isolate shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous-to-synonymous SNPs include two AP2 transcription factors and the P. vivax multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in Plasmodium falciparum. This analysis provides a data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies.
间日疟原虫引起全世界 25-40%的疟疾病例，但对这种人类疟原虫的研究却被忽视了。然而，最近间日疟原虫参考基因组的发表现在允许基因组学和系统生物学方法应用于这种病原体。我们在这里表明，可以直接从体外分离的寄生虫中进行寄生虫全基因组分析，而无需体外繁殖。从秘鲁一位患有临床疟疾的发热患者中获得的单个间日疟原虫分离株进行了全基因组测序（30×覆盖率）。这项分析揭示了超过 18261 个单核苷酸多态性（SNP），其中 6257 个进一步使用平铺微阵列进行了验证。在核心染色体基因中，我们发现每 985 个编码序列中的一个 SNP 将这种最近的秘鲁分离株 IQ07 与 1972 年获得的参考萨尔瓦多 I 株区分开来。这个未培养的间日疟原虫分离株的全基因组序列表明，通过基因组微阵列分析，具有低数量对齐测序reads 的相同区域也是高度可变的。最后，我们表明，包含最大非同义到同义 SNP 比例的基因包括两个 AP2 转录因子和间日疟原虫多药耐药相关蛋白（PvMRP1），ABC 转运蛋白被证明与恶性疟原虫中的奎宁和抗叶酸耐药性相关。这项分析提供了一个数据集，用于比较分析，具有识别全球寄生虫多样性和药物耐药性映射研究标记的重要潜力。
