Whole-genome sequencing and analysis of Plasmodium falciparum isolates from China-Myanmar border area

Shen, Hai-Mo; Chen, Shen-Bo; Cui, Yan-Bing; Xu, Bin; Kassegne, Kokouvi; Abe, Eniola Michael; Wang, Yue; Chen, Jun-Hu

doi:10.1186/s40249-018-0493-5

Cited by 17 publications

(17 citation statements)

References 39 publications

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“…For our analyses, genome and annotation data of Pf 3D7 strain (the most complete whole genome standard reference) from PlasmoDB database (http://plasmodb.org/plasmo/) (14) were downloaded. In addition, raw sequences from 62 genome data of falciparum clinical isolates from Africa [n = 32 (Congo DR, Gambia, Ghana, Guinea, Malawi, Mali, Nigeria, and Senegal)] and Asia [n = 30 (Bangladesh, Cambodia, China-Myanmar Border (CMB), Laos, Myanmar, Thailand, and Viet Nam)] were also referenced (15)(16)(17).…”

Section: Genomic Datamentioning

confidence: 99%

“…The fragmented DNA molecules were used to construct Illumina-sequencing libraries with TruSeq DNA LT Sample Prep Kit (Illumina). All libraries were sequenced on the Illumina HiSeq X10 platform according to the manufacturer's protocol (18), using the direct sequencing approach, as described previously (17). All reads were filtered by removing the adapter sequences and low quality sequences were removed with Trimmomatic-3.0.…”

Section: Whole-genome Sequencingmentioning

confidence: 99%

“…Principal component analysis (PCA) and neighbor-joining were performed to investigate major geographical division of population structure. PCA and a neighbor-joining tree of all samples were undertaken via SPSS-Ver25 and Mega-Ver6.0 programs, respectively, to compare Pf SNPs from Togo isolates with those from the 62 isolates collected worldwide (15)(16)(17).…”

Section: Identification Of Snps and Population Structurementioning

confidence: 99%

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Genome-Wide Analysis of the Malaria Parasite Plasmodium falciparum Isolates From Togo Reveals Selective Signals in Immune Selection-Related Antigen Genes

et al. 2020

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rosetting. This is consistent with expectations that elevated signals of selection due to allele-specific acquired immunity are likely to operate on antigenic targets. Collectively, our data suggest a recent expansion of Pf population in Togo and evidence strong host immune selection on membrane/surface antigens reflected in signals of balancing/positive selection of important gene loci. Findings from this study provide a fundamental basis to engage studies for effective malaria control in Togo.

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Section: Genomic Datamentioning

confidence: 99%

Section: Whole-genome Sequencingmentioning

confidence: 99%

Section: Identification Of Snps and Population Structurementioning

confidence: 99%

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Genome-Wide Analysis of the Malaria Parasite Plasmodium falciparum Isolates From Togo Reveals Selective Signals in Immune Selection-Related Antigen Genes

et al. 2020

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“…The addition of SLOPE to our laboratory toolset will be useful not only for proteomic and metabolomics studies (see above) but also genomic and transcriptomic analyses. Reduction of contaminating host DNA and RNA that remain associated with erythrocytes relative to parasite material will lead to increased sequencing coverage particularly in clinical samples, which contain a considerable human contribution 44 .…”

Section: Discussionmentioning

confidence: 99%

Cholesterol-dependent enrichment of understudied erythrocytic stages of human Plasmodium parasites

Brown

Moore

Guler

2020

Sci Rep

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for intracellular pathogens, the host cell provides needed protection and nutrients. A major challenge of intracellular parasite research is collection of high parasite numbers separated from host contamination. This situation is exemplified by the malaria parasite, which spends a substantial part of its life cycle inside erythrocytes as rings, trophozoites, and schizonts, before egress and reinvasion. erythrocytic Plasmodium parasite forms refractory to enrichment remain understudied due to high host contamination relative to low parasite numbers. Here, we present a method for separating all stages of Plasmodium-infected erythrocytes through lysis and removal of uninfected erythrocytes. The Streptolysin O-Percoll (SLOPE) method is effective on previously inaccessible forms, including circulating rings from malaria-infected patients and artemisinin-induced quiescent parasites. SLope can be used on multiple parasite species, under multiple media formulations, and lacks measurable impacts on parasite viability. We demonstrate erythrocyte membrane cholesterol levels modulate the preferential lysis of uninfected host cells by SLO, and therefore modulate the effectiveness of SLOPE. Targeted metabolomics of SLOPE-enriched ring stage samples confirms parasite-derived metabolites are increased and contaminating host material is reduced compared to non-enriched samples. Due to consumption of cholesterol by other intracellular bacteria and protozoa, SLope holds potential for improving research on organisms beyond Plasmodium. Malaria, caused by protozoan parasites of the Plasmodium genus, is a continuing threat to global health. A total of five Plasmodium species cause malaria in humans, with Plasmodium falciparum being responsible for the large majority of malaria morbidity and mortality 1. While the global malaria burden has decreased over the past decade, the emergence and spread of antimalarial resistant Plasmodium threatens to undo this progress and emphasizes the dire need to understand more about the biology of this parasite. The current World Health Organization recommendation for treatment of malaria is artemisinin combination therapy 2. However, clinical resistance has now been reported to both artemisinin and almost all of its partner drugs 3-5. All symptoms of malaria, including cyclical fevers and hypoglycemia, occur due to the asexual replication cycle of the parasite within human erythrocytes (Fig. 1a). Parasites undergo rounds of replication progressing from the ring stage, to trophozoites and schizonts, before rupturing from host erythrocytes to release merozoites, which go on to invade new erythrocytes and continue the cycle of infection 6. Many studies aiming to understand the biology of asexual Plasmodium are performed only on late stage parasite samples (trophozoites and schizonts). This is due in part to the larger biomass of these stages but also to the existence of effective enrichment methods 7 ; erythrocytes infected with late stage parasites can be separated from uninfected erythrocytes by density...

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“…To compare the previously simulated and observed data based on summary statistics, we used the ape [98] and pegas [99] libraries in R to estimate the number of polymorphic sites and the Tajima’s D based on the entire genomes. Tajima’s D is commonly used to estimate demographic changes in populations [100, 101]. Also, we obtained 1,000 sliding windows frames to estimate the Tajima’s D along the genomes, as well as the mean and standard deviation of Tajima’s D .…”

Section: Methodsmentioning

confidence: 99%

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

Vázquez-Rosas-Landa

Ponce-Soto

Aguirre‐Liguori

et al. 2019

Preprint

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323 words). 27 Background: In bacteria, pan-genomes are the result of the evolutionary "tug of 28 war" between selection and horizontal gene transfer (HGT). High rates of HGT 29 increase the genetic pool and the effective population size, resulting in open pan-30 genomes. In contrast, selective pressures can lead to local adaptation by purging 31 the variation introduced by HGT, resulting in closed pan-genomes and clonal 32 lineages. In this study, we explored both hypotheses elucidating the pan-genome 33 of Vibrionaceae isolates after a perturbation event in the endangered oasis of 34 Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the 35 environments in their genomes.36Results: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two 37 of them did not showed any close reference strain in databases. Five of the 38 lineages showed closed pan-genomes and were associated to either water or 39 sediment environment; their high effective population size (Ne) estimates suggest 40 that these lineages are not from a recent origin. The only clade with an open pan-41 genome was found in both environments and was formed by ten genetic groups 42 with low Ne, suggesting a recent origin. The recombination and mutation estimators 43 (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae 44 estimations; however, we identified 367 gene families with signals of positive 45 selection, most of them found in the core genome; suggesting that despite 46 recombination, natural selection moves the Vibrionaceae CCB lineages to local 47 adaptation purging the genomes and keeping closed pan-genome patterns. 48 Moreover, we identify 598 SNPs associated with an unstructured environment; 49 some of the genes under this SNPs were related to sodium transport. 50 Conclusions: Different lines of evidence suggest that the sampled Vibrionaceae, 51 are part of the rare biosphere usually living under famine conditions. Two of these 52 lineages were reported by the first time. Most Vibrionaceae lineages of CCB are 53 adapted to their microhabitats rather than to the sampled environments. This 54 pattern of adaptation agrees with the association of closed pan-genomes and local 55 adaptation. 56 57 3Comparative genomics analyses have shown a wide range of genomic 78 variation within bacteria from different phylogenetic groups [1][2][3]. This variation 79 range has been explained in part by the wide ecological niche occupied by different 80 bacterial groups [4][5][6][7][8]. Bacterial genomes, in contrast to eukaryotic genomes, 81 usually maintain constant genome sizes [9, 10], suggesting that while horizontal 82 gene transfer (HGT) increases the genome size by adding new genes, selection 83 maintains the genome size by removing deleterious, non-functional or non-useful 84 genes [11][12][13]. Therefore, bacteria can present very different genomic 85 compositions even within a species, with HGT creating a flexible genome and 86 natural selection purging or maintaining it [10, 14]. 87...

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Whole-genome sequencing and analysis of Plasmodium falciparum isolates from China-Myanmar border area

Cited by 17 publications

References 39 publications

Genome-Wide Analysis of the Malaria Parasite Plasmodium falciparum Isolates From Togo Reveals Selective Signals in Immune Selection-Related Antigen Genes

Genome-Wide Analysis of the Malaria Parasite Plasmodium falciparum Isolates From Togo Reveals Selective Signals in Immune Selection-Related Antigen Genes

Cholesterol-dependent enrichment of understudied erythrocytic stages of human Plasmodium parasites

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

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