Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes

@article{Dharia2010WholegenomeSA,
  title={Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes},
  author={Neekesh V. Dharia and Andrew Bright and Scott Westenberger and S. Whitney Barnes and Sergei Batalov and Kelli L. Kuhen and Rachel Borboa and Glenn C Federe and Colleen M. McClean and Joseph Michael Vinetz and Victor Neyra and Alejandro Llanos-Cuentas and John W. Barnwell and John R. Walker and Elizabeth A. Winzeler},
  journal={Proceedings of the National Academy of Sciences},
  year={2010},
  volume={107},
  pages={20045 - 20050}
}
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… 

Figures and Tables from this paper

Whole genome sequencing analysis of Plasmodium vivax using whole genome capture BMC Genomics
TLDR
It is shown that in-solution hybridization capture can be used to extract P. vivax DNA from human contaminating DNA in the laboratory without the need for on-site leukocyte filtration and will enable more efficient whole genome analysis of P.vivax from a larger geographic region and from valuable archived sample collections.
Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes.
TLDR
The data suggest that whole genome sequencing of malaria parasites from patients may provide more insight about the evolution of drug resistance than genetic linkage or association studies, especially in geographical regions with limited parasite genetic diversity.
The biology of Plasmodium vivax explored through genomics
TLDR
The authors' comparative genomic analysis of five P. vivax reference genomes and several whole‐genome sequences of the closely related monkey malaria species P. cynomolgi has revealed an extraordinary level of genetic diversity and enabled characterization of novel multigene families and important single‐copy genes.
Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax
TLDR
This study shows that it is feasible to perform whole genome sequencing of P. vivax field isolates and rigorously characterize the genetic diversity of this parasite, and identifies more than 80,000 SNPs distributed throughout the genome which will allow designing association studies and population surveys.
Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia
TLDR
The whole-genome study of P. vivax from Cordóba, Colombia, shows that the parasite population is genetically diverse, which is contrary to expectations from earlier studies from the Americas, and finds molecular evidence that resistance to an anti-malarial drug has arisen recently in this region.
Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
TLDR
The whole genome capture technique will enable more efficient whole genome analysis of P. vivax from a larger geographic region and from valuable archived sample collections and will allow study of the evolution and population biology of the parasite, allow parasite transmission patterns to be characterized, and may facilitate the identification of new drug resistance genes.
Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains
TLDR
The discovery of a duplication of the P. vivax Duffy binding protein (PvDBP) gene suggests that PvDBP, a merozoite surface protein involved in red cell adhesion is rapidly evolving, possibly in response to constraints imposed by erythrocyte Duffy negativity in some human populations.
Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing
TLDR
In 22 P. vivax patient isolates prepared with the 2-step method, high depth (median 654X coverage) and breadth (≥89%) of coverage on the Illumina GAII and HiSeq platforms are demonstrated and negligible bias was observed in coverage depth between coding and non-coding regions of the P.vivax genome.
Whole Genome Sequencing of Plasmodium vivax Isolates Reveals Frequent Sequence and Structural Polymorphisms in Erythrocyte Binding Genes
TLDR
Single nucleotide polymorphism and copy number variation in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia showed various levels of gene flow at a small geographical scale, and allowed a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale.
Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure
Background Although Plasmodium vivax contributes to almost half of all malaria cases outside Africa, it has been relatively neglected compared to the more deadly P. falciparum. It is known that P.
...
...

References

SHOWING 1-10 OF 59 REFERENCES
Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages.
Comparative genomics of the neglected human malaria parasite Plasmodium vivax
TLDR
The synteny and isochore structure of P. vivax chromosomes are described, and it is shown that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously.
Genome sequence of the human malaria parasite Plasmodium falciparum
TLDR
The genome sequence of P. falciparum clone 3D7 is reported, which is the most (A + T)-rich genome sequenced to date and is being exploited in the search for new drugs and vaccines to fight malaria.
A genome-wide map of diversity in Plasmodium falciparum
TLDR
An initial survey of genetic variation across the P. falciparum genome is described and its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite is demonstrated.
A Systematic Map of Genetic Variation in Plasmodium falciparum
TLDR
It is speculated that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs.
Genome variation and evolution of the malaria parasite Plasmodium falciparum
TLDR
This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum–P.
A Systems-Based Analysis of Plasmodium vivax Lifecycle Transcription from Human to Mosquito
TLDR
This work examined parasite transcriptional changes in samples from infected patients and mosquitoes in order to characterize gene function, define regulatory sequences and reveal new potential vaccine candidate genes, concluding that high-quality gene expression data can be readily obtained directly from patient samples and that many of the same uncharacterized genes that are up regulated in different P. vivax lifecycle stages are also upregulated in similar stages in other Plasmodium species.
The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites
TLDR
The complete transcriptional profile throughout the 48-h intraerythrocytic cycle of three distinct P. vivax isolates is presented, identifying strain specific patterns of expression for subsets of genes predicted to encode proteins associated with virulence and host pathogen interactions.
Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome
TLDR
This work surveyed P. falciparum genes for polymorphisms and identified various highly polymorphic loci and genes, some of which encode new antigens that are confirmed using human immune sera and providing urgently needed vaccine candidates for disease control.
...
...