SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics
Abstract Background Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however m...
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ftdoajarticles:oai:doaj.org/article:47c2a8a7586e429bb5e17b5cb1a7b59f 2023-05-15T15:15:16+02:00 SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics Abebe A. Fola Eline Kattenberg Zahra Razook Dulcie Lautu-Gumal Stuart Lee Somya Mehra Melanie Bahlo James Kazura Leanne J. Robinson Moses Laman Ivo Mueller Alyssa E. Barry 2020-10-01T00:00:00Z https://doi.org/10.1186/s12936-020-03440-0 https://doaj.org/article/47c2a8a7586e429bb5e17b5cb1a7b59f EN eng BMC http://link.springer.com/article/10.1186/s12936-020-03440-0 https://doaj.org/toc/1475-2875 doi:10.1186/s12936-020-03440-0 1475-2875 https://doaj.org/article/47c2a8a7586e429bb5e17b5cb1a7b59f Malaria Journal, Vol 19, Iss 1, Pp 1-15 (2020) Malaria Plasmodium vivax Microsatellites Single Nucleotide Polymorphisms (SNPs) Diversity Population structure Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2020 ftdoajarticles https://doi.org/10.1186/s12936-020-03440-0 2022-12-31T11:04:03Z Abstract Background Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since ‘universal’ barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. Methods Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. Results From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56–7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 19 1 |
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topic |
Malaria Plasmodium vivax Microsatellites Single Nucleotide Polymorphisms (SNPs) Diversity Population structure Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Malaria Plasmodium vivax Microsatellites Single Nucleotide Polymorphisms (SNPs) Diversity Population structure Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Abebe A. Fola Eline Kattenberg Zahra Razook Dulcie Lautu-Gumal Stuart Lee Somya Mehra Melanie Bahlo James Kazura Leanne J. Robinson Moses Laman Ivo Mueller Alyssa E. Barry SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics |
topic_facet |
Malaria Plasmodium vivax Microsatellites Single Nucleotide Polymorphisms (SNPs) Diversity Population structure Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
Abstract Background Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since ‘universal’ barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. Methods Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. Results From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56–7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to ... |
format |
Article in Journal/Newspaper |
author |
Abebe A. Fola Eline Kattenberg Zahra Razook Dulcie Lautu-Gumal Stuart Lee Somya Mehra Melanie Bahlo James Kazura Leanne J. Robinson Moses Laman Ivo Mueller Alyssa E. Barry |
author_facet |
Abebe A. Fola Eline Kattenberg Zahra Razook Dulcie Lautu-Gumal Stuart Lee Somya Mehra Melanie Bahlo James Kazura Leanne J. Robinson Moses Laman Ivo Mueller Alyssa E. Barry |
author_sort |
Abebe A. Fola |
title |
SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics |
title_short |
SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics |
title_full |
SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics |
title_fullStr |
SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics |
title_full_unstemmed |
SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics |
title_sort |
snp barcodes provide higher resolution than microsatellite markers to measure plasmodium vivax population genetics |
publisher |
BMC |
publishDate |
2020 |
url |
https://doi.org/10.1186/s12936-020-03440-0 https://doaj.org/article/47c2a8a7586e429bb5e17b5cb1a7b59f |
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Arctic |
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Arctic |
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Arctic |
op_source |
Malaria Journal, Vol 19, Iss 1, Pp 1-15 (2020) |
op_relation |
http://link.springer.com/article/10.1186/s12936-020-03440-0 https://doaj.org/toc/1475-2875 doi:10.1186/s12936-020-03440-0 1475-2875 https://doaj.org/article/47c2a8a7586e429bb5e17b5cb1a7b59f |
op_doi |
https://doi.org/10.1186/s12936-020-03440-0 |
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Malaria Journal |
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19 |
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1766345630134829056 |