Rapid whole genome optical mapping of Plasmodium falciparum
Abstract Background Immune evasion and drug resistance in malaria have been linked to chromosomal recombination and gene copy number variation (CNV). These events are ideally studied using comparative genomic analyses; however in malaria these analyses are not as common or thorough as in other infec...
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ftdoajarticles:oai:doaj.org/article:6948ae8de9ad4a1ebbfe2a7a426ab00f 2023-05-15T15:14:11+02:00 Rapid whole genome optical mapping of Plasmodium falciparum Johnson Jake D Kirkup Benjamin C Riley Matthew C Lesho Emil P Ockenhouse Christian F 2011-08-01T00:00:00Z https://doi.org/10.1186/1475-2875-10-252 https://doaj.org/article/6948ae8de9ad4a1ebbfe2a7a426ab00f EN eng BMC http://www.malariajournal.com/content/10/1/252 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-10-252 1475-2875 https://doaj.org/article/6948ae8de9ad4a1ebbfe2a7a426ab00f Malaria Journal, Vol 10, Iss 1, p 252 (2011) Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2011 ftdoajarticles https://doi.org/10.1186/1475-2875-10-252 2022-12-31T13:13:50Z Abstract Background Immune evasion and drug resistance in malaria have been linked to chromosomal recombination and gene copy number variation (CNV). These events are ideally studied using comparative genomic analyses; however in malaria these analyses are not as common or thorough as in other infectious diseases, partly due to the difficulty in sequencing and assembling complete genome drafts. Recently, whole genome optical mapping has gained wide use in support of genomic sequence assembly and comparison. Here, a rapid technique for producing whole genome optical maps of Plasmodium falciparum is described and the results of mapping four genomes are presented. Methods Four laboratory strains of P. falciparum were analysed using the Argus™ optical mapping system to produce ordered restriction fragment maps of all 14 chromosomes in each genome. Plasmodium falciparum DNA was isolated directly from blood culture, visualized using the Argus™ system and assembled in a manner analogous to next generation sequence assembly into maps (AssemblyViewer™, OpGen Inc. ® ). Full coverage maps were generated for P. falciparum strains 3D7, FVO, D6 and C235. A reference P. falciparum in silico map was created by the digestion of the genomic sequence of P. falciparum with the restriction enzyme AflII, for comparisons to genomic optical maps. Maps were then compared using the MapSolver™ software. Results Genomic variation was observed among the mapped strains, as well as between the map of the reference strain and the map derived from the putative sequence of that same strain. Duplications, deletions, insertions, inversions and misassemblies of sizes ranging from 3,500 base pairs up to 78,000 base pairs were observed. Many genomic events occurred in areas of known repetitive sequence or high copy number genes, including var gene clusters and rifin complexes. Conclusions This technique for optical mapping of multiple malaria genomes allows for whole genome comparison of multiple strains and can assist in identifying genetic ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 10 1 |
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Directory of Open Access Journals: DOAJ Articles |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Johnson Jake D Kirkup Benjamin C Riley Matthew C Lesho Emil P Ockenhouse Christian F Rapid whole genome optical mapping of Plasmodium falciparum |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
Abstract Background Immune evasion and drug resistance in malaria have been linked to chromosomal recombination and gene copy number variation (CNV). These events are ideally studied using comparative genomic analyses; however in malaria these analyses are not as common or thorough as in other infectious diseases, partly due to the difficulty in sequencing and assembling complete genome drafts. Recently, whole genome optical mapping has gained wide use in support of genomic sequence assembly and comparison. Here, a rapid technique for producing whole genome optical maps of Plasmodium falciparum is described and the results of mapping four genomes are presented. Methods Four laboratory strains of P. falciparum were analysed using the Argus™ optical mapping system to produce ordered restriction fragment maps of all 14 chromosomes in each genome. Plasmodium falciparum DNA was isolated directly from blood culture, visualized using the Argus™ system and assembled in a manner analogous to next generation sequence assembly into maps (AssemblyViewer™, OpGen Inc. ® ). Full coverage maps were generated for P. falciparum strains 3D7, FVO, D6 and C235. A reference P. falciparum in silico map was created by the digestion of the genomic sequence of P. falciparum with the restriction enzyme AflII, for comparisons to genomic optical maps. Maps were then compared using the MapSolver™ software. Results Genomic variation was observed among the mapped strains, as well as between the map of the reference strain and the map derived from the putative sequence of that same strain. Duplications, deletions, insertions, inversions and misassemblies of sizes ranging from 3,500 base pairs up to 78,000 base pairs were observed. Many genomic events occurred in areas of known repetitive sequence or high copy number genes, including var gene clusters and rifin complexes. Conclusions This technique for optical mapping of multiple malaria genomes allows for whole genome comparison of multiple strains and can assist in identifying genetic ... |
format |
Article in Journal/Newspaper |
author |
Johnson Jake D Kirkup Benjamin C Riley Matthew C Lesho Emil P Ockenhouse Christian F |
author_facet |
Johnson Jake D Kirkup Benjamin C Riley Matthew C Lesho Emil P Ockenhouse Christian F |
author_sort |
Johnson Jake D |
title |
Rapid whole genome optical mapping of Plasmodium falciparum |
title_short |
Rapid whole genome optical mapping of Plasmodium falciparum |
title_full |
Rapid whole genome optical mapping of Plasmodium falciparum |
title_fullStr |
Rapid whole genome optical mapping of Plasmodium falciparum |
title_full_unstemmed |
Rapid whole genome optical mapping of Plasmodium falciparum |
title_sort |
rapid whole genome optical mapping of plasmodium falciparum |
publisher |
BMC |
publishDate |
2011 |
url |
https://doi.org/10.1186/1475-2875-10-252 https://doaj.org/article/6948ae8de9ad4a1ebbfe2a7a426ab00f |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 10, Iss 1, p 252 (2011) |
op_relation |
http://www.malariajournal.com/content/10/1/252 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-10-252 1475-2875 https://doaj.org/article/6948ae8de9ad4a1ebbfe2a7a426ab00f |
op_doi |
https://doi.org/10.1186/1475-2875-10-252 |
container_title |
Malaria Journal |
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10 |
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1 |
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1766344673940471808 |