Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar Border
Plasmodium falciparum isolates from China–Myanmar border (CMB) have experienced regional special selective pressures and adaptive evolution. However, the genomes of P. falciparum isolates from this region to date are poorly characterized. Herein, we performed whole-genome sequencing of 34 P. falcipa...
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Frontiers Media S.A.
2019-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.01065/full |
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| author | Run Ye Yini Tian Yufu Huang Yilong Zhang Jian Wang Xiaodong Sun Hongning Zhou Dongmei Zhang Weiqing Pan |
| author_facet | Run Ye Yini Tian Yufu Huang Yilong Zhang Jian Wang Xiaodong Sun Hongning Zhou Dongmei Zhang Weiqing Pan |
| author_sort | Run Ye |
| collection | DOAJ |
| description | Plasmodium falciparum isolates from China–Myanmar border (CMB) have experienced regional special selective pressures and adaptive evolution. However, the genomes of P. falciparum isolates from this region to date are poorly characterized. Herein, we performed whole-genome sequencing of 34 P. falciparum isolates from CMB and a series of genome-wide sequence analyses to reveal their genetic diversity, population structures, and comparisons with the isolates from other epidemic regions (Thai–Cambodia border, Thai–Myanmar border, and West Africa). Totally 59,720 high-quality single-nucleotide polymorphisms (SNPs) were identified in the P. falciparum isolates from CMB, with average nucleotide diversity (π = 4.59 × 10−4) and LD decay (132 bp). The Tajima’s D and Fu and Li’s D values of the CMB isolates were −0.8 (p < 0.05) and −0.84 (p < 0.05), respectively, suggesting a demographic history of recent population expansion or purifying selection. Moreover, 78 genes of the parasite were identified that could be under positive selection, including those genes conferring drug resistance such as pfubp1. In addition, 33 SNPs were identified for tracing the source of the parasites with a high accuracy by analysis of the most differential SNPs among the four epidemic regions. Collectively, our data demonstrated high diversity of the CMB isolates’ genomes forming a distinct population, and the identification of 33-SNP barcode provides a valuable surveillance of parasite migration among the regions. |
| first_indexed | 2024-12-11T10:01:10Z |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-11T10:01:10Z |
| publishDate | 2019-10-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-3e5f07970ebb44e2a49906caf51588d62022-12-22T01:12:06ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-10-011010.3389/fgene.2019.01065478316Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar BorderRun Ye0Yini Tian1Yufu Huang2Yilong Zhang3Jian Wang4Xiaodong Sun5Hongning Zhou6Dongmei Zhang7Weiqing Pan8Department of Tropical Diseases, Naval Medical University, Shanghai, ChinaDepartment of Tropical Diseases, Naval Medical University, Shanghai, ChinaDepartment of Tropical Diseases, Naval Medical University, Shanghai, ChinaDepartment of Tropical Diseases, Naval Medical University, Shanghai, ChinaYunnan Institute of Parasitic Diseases, Puer, ChinaYunnan Institute of Parasitic Diseases, Puer, ChinaYunnan Institute of Parasitic Diseases, Puer, ChinaDepartment of Tropical Diseases, Naval Medical University, Shanghai, ChinaDepartment of Tropical Diseases, Naval Medical University, Shanghai, ChinaPlasmodium falciparum isolates from China–Myanmar border (CMB) have experienced regional special selective pressures and adaptive evolution. However, the genomes of P. falciparum isolates from this region to date are poorly characterized. Herein, we performed whole-genome sequencing of 34 P. falciparum isolates from CMB and a series of genome-wide sequence analyses to reveal their genetic diversity, population structures, and comparisons with the isolates from other epidemic regions (Thai–Cambodia border, Thai–Myanmar border, and West Africa). Totally 59,720 high-quality single-nucleotide polymorphisms (SNPs) were identified in the P. falciparum isolates from CMB, with average nucleotide diversity (π = 4.59 × 10−4) and LD decay (132 bp). The Tajima’s D and Fu and Li’s D values of the CMB isolates were −0.8 (p < 0.05) and −0.84 (p < 0.05), respectively, suggesting a demographic history of recent population expansion or purifying selection. Moreover, 78 genes of the parasite were identified that could be under positive selection, including those genes conferring drug resistance such as pfubp1. In addition, 33 SNPs were identified for tracing the source of the parasites with a high accuracy by analysis of the most differential SNPs among the four epidemic regions. Collectively, our data demonstrated high diversity of the CMB isolates’ genomes forming a distinct population, and the identification of 33-SNP barcode provides a valuable surveillance of parasite migration among the regions.https://www.frontiersin.org/article/10.3389/fgene.2019.01065/fullPlasmodium falciparumgenomesChina–Myanmar borderdiversitygenetic marker |
| spellingShingle | Run Ye Yini Tian Yufu Huang Yilong Zhang Jian Wang Xiaodong Sun Hongning Zhou Dongmei Zhang Weiqing Pan Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar Border Frontiers in Genetics Plasmodium falciparum genomes China–Myanmar border diversity genetic marker |
| title | Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar Border |
| title_full | Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar Border |
| title_fullStr | Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar Border |
| title_full_unstemmed | Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar Border |
| title_short | Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China–Myanmar Border |
| title_sort | genome wide analysis of genetic diversity in plasmodium falciparum isolates from china myanmar border |
| topic | Plasmodium falciparum genomes China–Myanmar border diversity genetic marker |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.01065/full |
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