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Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi

Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination prog...

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Autores principales: Mathema, Vivek Bhakta, Nakeesathit, Supatchara, White, Nicholas J., Dondorp, Arjen M., Imwong, Mallika
Formato: Online Artículo Texto
Lenguaje:English
Publicado: EDP Sciences 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227371/
https://www.ncbi.nlm.nih.gov/pubmed/32410726
http://dx.doi.org/10.1051/parasite/2020034
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author Mathema, Vivek Bhakta
Nakeesathit, Supatchara
White, Nicholas J.
Dondorp, Arjen M.
Imwong, Mallika
author_facet Mathema, Vivek Bhakta
Nakeesathit, Supatchara
White, Nicholas J.
Dondorp, Arjen M.
Imwong, Mallika
author_sort Mathema, Vivek Bhakta
collection PubMed
description Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1–10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18–29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms “cell parts,” “binding,” “developmental processes,” and “metabolic processes.” The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology.
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spelling pubmed-72273712020-05-20 Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi Mathema, Vivek Bhakta Nakeesathit, Supatchara White, Nicholas J. Dondorp, Arjen M. Imwong, Mallika Parasite Research Article Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1–10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18–29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms “cell parts,” “binding,” “developmental processes,” and “metabolic processes.” The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology. EDP Sciences 2020-05-15 /pmc/articles/PMC7227371/ /pubmed/32410726 http://dx.doi.org/10.1051/parasite/2020034 Text en © V.B. Mathema et al., published by EDP Sciences, 2020 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Mathema, Vivek Bhakta
Nakeesathit, Supatchara
White, Nicholas J.
Dondorp, Arjen M.
Imwong, Mallika
Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi
title Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi
title_full Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi
title_fullStr Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi
title_full_unstemmed Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi
title_short Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi
title_sort genome-wide microsatellite characteristics of five human plasmodium species, focusing on plasmodium malariae and p. ovale curtisi
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227371/
https://www.ncbi.nlm.nih.gov/pubmed/32410726
http://dx.doi.org/10.1051/parasite/2020034
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