Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism
Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored th...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | en |
| Published: |
Plos One Publishing
2015
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| Subjects: | |
| Online Access: | http://ir.unimas.my/id/eprint/10714/1/Plasmodium.pdf http://ir.unimas.my/id/eprint/10714/ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121303 |
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| Summary: | Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population
that can be severe and fatal. The study of P. knowlesi parasites from human clinical
isolates is relatively new and, in order to obtain maximum information from patient sample
collections, we explored the possibility of generating P. knowlesi genome sequences from
archived clinical isolates. Our patient sample collection consisted of frozen whole blood
samples that contained excessive human DNA contamination and, in that form, were not
suitable for parasite genome sequencing. We developed a method to reduce the amount of
human DNA in the thawed blood samples in preparation for high throughput parasite genome
sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen
samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing.
The reads were mapped to the P. knowlesi H strain reference genome and an average mapping
of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for
subsequent analyses. Previously we identified a DNA sequence dimorphism on a small
fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We
used the genome data to assemble full-length Pknbpxa sequences and discovered that the
dimorphism extended along the gene. An in-house algorithm was developed to detect SNP
sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic,
involving genes on all chromosomes and suggesting that two distinct types of
P. knowlesi infect the human population in Sarawak, Malaysian Borneo.We use P. knowlesi
clinical samples to demonstrate that Plasmodium DNA from archived patient samples can
produce high quality genome data.We show that analyses, of even small numbers of difficult
clinical malaria isolates, can generate comprehensive genomic information that will improve
our understanding of malaria parasite diversity and pathobiology. |
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