De novo assembly of a field isolate genome reveals novel Plasmodium vivax erythrocyte invasion genes.
De novo assembly of a field isolate genome reveals novel Plasmodium vivax erythrocyte invasion genes.
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DOI：
10.1371/journal.pntd.0002569
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发表时间：
2013
影响因子：
3.8
通讯作者：
Serre D
中科院分区：
文献类型：
--
作者：
Hester J;Chan ER;Menard D;Mercereau-Puijalon O;Barnwell J;Zimmerman PA;Serre D
最近间日疟原虫野外分离株和猴适应株的测序使整个基因组的SNP特征化成为可能。这些分析依赖于将短读段映射到间日疟原虫参考基因组上，该参考基因组是使用来自猴适应菌株萨尔瓦多I的DNA生成的。在该菌株中缺失的任何基因组基因座将在参考基因组序列中缺失并且在先前的分析中缺失。在这里，我们报告从头组装的间日疟原虫田间分离株基因组。在2，857个组装的重叠群中，我们鉴定了362个重叠群，每个重叠群含有超过5 kb的参考基因组序列中不存在的连续DNA序列。这些新的间日疟原虫DNA序列占380万个核苷酸，包含792个预测基因。这些重叠群中的大多数包含多基因家族的成员，并且可能起源于端粒区域。有趣的是，我们确定了两个重叠群含有预测的蛋白质编码基因类似于已知的疟原虫红细胞入侵蛋白。一个基因编码与食蟹猴毕赤酵母RBP 2 e和诺氏毕赤酵母NBPXb正交的网织红细胞结合蛋白基因。第二个基因具有疟原虫红细胞结合蛋白的所有特征，包括保守的Duffy结合样和C-末端富含半胱氨酸的结构域。系统发育分析表明，这个新的基因簇分别从所有已知的疟原虫达菲结合蛋白基因。其他分析表明，该基因存在于大多数间日疟原虫基因组中，并在血液阶段寄生虫中转录，这表明间日疟原虫红细胞入侵机制可能比目前所了解的更为复杂。这里采用的策略补充了以前的基因组分析，并充分利用了下一代测序数据，以提供这种重要疟疾寄生虫遗传变异的全面表征。通过从头组装发现的新蛋白质编码基因的进一步分析有可能鉴定影响间日疟原虫生物学关键方面的基因，包括人类红细胞侵袭的替代机制。 间日疟原虫是非洲以外的大多数疟疾病例的罪魁祸首，但人们对它的了解很少，因为这种寄生虫很难在体外进行研究。基因组测序研究提供了一个新的和令人兴奋的机会，以更好地了解这种寄生虫，但到目前为止，直接映射到参考基因组序列从一个单一的P.间日疟原虫菌株。在这里，我们使用从现场分离产生的序列数据来重建长DNA序列，而不依赖于参考基因组。我们的分析揭示了许多参考基因组中不存在的间日疟原虫DNA序列，包含792个预测基因。这些新基因之一编码一种预测的蛋白质，类似于已知的疟原虫蛋白质参与红细胞入侵。这种新基因存在于迄今为止测序的所有间日疟原虫菌株中，除了用于产生参考基因组的菌株，并且在血液阶段寄生虫中转录。总的来说，我们的分析表明，间日疟原虫基因的目录是不完整的，潜在的重要基因已经错过了。我们特别确定了一个假定的入侵基因，似乎功能，并可能大大改变我们的理解机制，确定红细胞入侵这种重要的疟疾寄生虫。
Recent sequencing of Plasmodium vivax field isolates and monkey-adapted strains enabled characterization of SNPs throughout the genome. These analyses relied on mapping short reads onto the P. vivax reference genome that was generated using DNA from the monkey-adapted strain Salvador I. Any genomic locus deleted in this strain would be lacking in the reference genome sequence and missed in previous analyses. Here, we report de novo assembly of a P. vivax field isolate genome. Out of 2,857 assembled contigs, we identify 362 contigs, each containing more than 5 kb of contiguous DNA sequences absent from the reference genome sequence. These novel P. vivax DNA sequences account for 3.8 million nucleotides and contain 792 predicted genes. Most of these contigs contain members of multigene families and likely originate from telomeric regions. Interestingly, we identify two contigs containing predicted protein coding genes similar to known Plasmodium red blood cell invasion proteins. One gene encodes the reticulocyte-binding protein gene orthologous to P. cynomolgi RBP2e and P. knowlesi NBPXb. The second gene harbors all the hallmarks of a Plasmodium erythrocyte-binding protein, including conserved Duffy-binding like and C-terminus cysteine-rich domains. Phylogenetic analysis shows that this novel gene clusters separately from all known Plasmodium Duffy-binding protein genes. Additional analyses showing that this gene is present in most P. vivax genomes and transcribed in blood-stage parasites suggest that P. vivax red blood cell invasion mechanisms may be more complex than currently understood. The strategy employed here complements previous genomic analyses and takes full advantage of next-generation sequencing data to provide a comprehensive characterization of genetic variations in this important malaria parasite. Further analyses of the novel protein coding genes discovered through de novo assembly have the potential to identify genes that influence key aspects of P. vivax biology, including alternative mechanisms of human erythrocyte invasion. Plasmodium vivax is responsible for most malaria cases outside Africa, but is poorly understood, as the parasite is difficult to study in vitro. Genome sequencing studies offer a novel and exciting opportunity to better understand this parasite but, so far, have directly mapped reads onto the reference genome sequence generated from a single P. vivax strain. Here, we use sequence data generated from a field isolate to reconstruct long DNA sequences without relying on the reference genome. Our analyses reveal many P. vivax DNA sequences that are absent from the reference genome and contain 792 predicted genes. One of these novel genes encodes a predicted protein similar to known Plasmodium proteins involved in red blood cell invasion. This new gene is present in all P. vivax strains sequenced so far, except for the strain used to generate the reference genome, and is transcribed in blood-stage parasites. Overall, our analyses show that the catalogue of P. vivax genes was incomplete and that potentially important genes have been missed. We notably identified one putative invasion gene that seems functional and could dramatically change our understanding of the mechanisms determining red blood cell invasion by this important malaria parasite.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
6.4
作者：
Carvalho, Bruna O.;Lopes, Stefanie C. P.;Costa, Fabio T. M.
通讯作者：
Costa, Fabio T. M.
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
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.
影响因子：
7.8
作者：
Gilberger, TW;Thompson, JK;Cowman, AF
通讯作者：
Cowman, AF