Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area.
Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area.
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DOI：
10.1186/s12864-017-3523-y
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发表时间：
2017-02-06
期刊：
影响因子：
4.4
通讯作者：
Chen JH
中科院分区：
文献类型：
--
作者：
Chen SB;Wang Y;Kassegne K;Xu B;Shen HM;Chen JH
目前，中国从东南亚输入的间日疟原虫病例呈上升趋势，特别是中缅边境地区。由于间日疟原虫病例的增加以及对疫苗和药物开发的更大需求，一些间日疟原虫分离株基因组测序项目正在进行中。然而，到目前为止，人们对这一地区的遗传变异性知之甚少。中缅边境地区首个间日疟原虫分离物（CMB-1）测序结果为1.2亿对末端reads。10.6个高质量评价reads的百分比与参考菌株Sal I基因组的99.9%一致，覆盖率为62倍，平均为4.8个snp / kb。我们提出了一个539 snp的间日疟原虫标记数据集，可以高灵敏度地识别来自不同地理来源的不同寄生虫。我们还发现，在RBP、SERA、vir、MSP3和AP2等多基因家族成员中，存在异常高水平的遗传变异。de-novo组装得到了一个由8409个序列组成的数据库，其中N50长度为6.6 kb，揭示了661个新的预测基因，其中包括78个vir基因，表明间日疟原虫来自该地区的功能差异更大。本研究结果有助于更好地理解间日疟的遗传变异，并为中缅边境地区间日疟的地理分化提供了基础依据。这种新的测序方法可作为间日疟原虫基因组研究的重要工具。本文的在线版本（doi:10.1186/s12864-017-3523-y）包含补充材料，授权用户可以使用。
Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now. The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area. Our result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future. The online version of this article (doi:10.1186/s12864-017-3523-y) contains supplementary material, which is available to authorized users.