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...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Plos One Publishing
2015
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| Subjects: | |
| Online Access: | http://ir.unimas.my/id/eprint/10714/ http://ir.unimas.my/id/eprint/10714/1/Plasmodium.pdf |
| _version_ | 1848836844052021248 |
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| author | Miguel M., Pinheiro Md Atique, Ahmed Scott B., Millar Theo, Sanderson Thomas, D. Otto Woon, Chan Lu Sanjeev, Krishna Julian C., Rayner Janet, Cox-Singh |
| author_facet | Miguel M., Pinheiro Md Atique, Ahmed Scott B., Millar Theo, Sanderson Thomas, D. Otto Woon, Chan Lu Sanjeev, Krishna Julian C., Rayner Janet, Cox-Singh |
| author_sort | Miguel M., Pinheiro |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-15T06:30:13Z |
| format | Article |
| id | unimas-10714 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T06:30:13Z |
| publishDate | 2015 |
| publisher | Plos One Publishing |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | unimas-107142022-01-28T02:27:27Z http://ir.unimas.my/id/eprint/10714/ Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism Miguel M., Pinheiro Md Atique, Ahmed Scott B., Millar Theo, Sanderson Thomas, D. Otto Woon, Chan Lu Sanjeev, Krishna Julian C., Rayner Janet, Cox-Singh R Medicine (General) 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. Plos One Publishing 2015 Article PeerReviewed text en http://ir.unimas.my/id/eprint/10714/1/Plasmodium.pdf Miguel M., Pinheiro and Md Atique, Ahmed and Scott B., Millar and Theo, Sanderson and Thomas, D. Otto and Woon, Chan Lu and Sanjeev, Krishna and Julian C., Rayner and Janet, Cox-Singh (2015) Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism. PLoS ONE, 10 (4). ISSN 1932-6203 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121303 doi:10.1371/journal.pone.0121303 |
| spellingShingle | R Medicine (General) Miguel M., Pinheiro Md Atique, Ahmed Scott B., Millar Theo, Sanderson Thomas, D. Otto Woon, Chan Lu Sanjeev, Krishna Julian C., Rayner Janet, Cox-Singh Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism |
| title | Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism |
| title_full | Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism |
| title_fullStr | Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism |
| title_full_unstemmed | Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism |
| title_short | Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism |
| title_sort | plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism |
| topic | R Medicine (General) |
| url | http://ir.unimas.my/id/eprint/10714/ http://ir.unimas.my/id/eprint/10714/ http://ir.unimas.my/id/eprint/10714/ http://ir.unimas.my/id/eprint/10714/1/Plasmodium.pdf |