Parasite genomics articles within Nature Communications

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  • Article
    | Open Access

    Host-parasite interactions can lead to negative frequency-dependent selection. Here, the authors sequence the genomes of H. bakeri and H. polygyrus, parasites of house and wood mice, respectively, and find that proteins that interact with the host immune response are often highly diverse.

    • Lewis Stevens
    • , Isaac Martínez-Ugalde
    •  & Mark Blaxter

  • Article
    | Open Access

    Sequencing malaria parasites from low density infections in small amounts of dried blood is important for large-scale genomic surveillance. Here, the authors develop and validate a highly multiplexed droplet digital PCR-based amplicon deep sequencing assay and apply it to data from Zanzibar, Tanzania.

    • Aurel Holzschuh
    • , Anita Lerch
    •  & Cristian Koepfli

  • Article
    | Open Access

    The ability to evolve Plasmodium drug resistance in vitro is challenging and time consuming. Here, Kümpornsin et al. generated a Plasmodium falciparum parasite line with an elevated mutation rate by impairing the proof-reading activity of DNA polymerase, which results in a higher mutation rate, quick resistance development, and a lower inoculum than wild type to support the identification of new antimalarial targets and understand drug resistance mechanisms.

    • Krittikorn Kümpornsin
    • , Theerarat Kochakarn
    •  & Marcus C. S. Lee

  • Article
    | Open Access

    In this work, susceptibilities to two key antimalarials, dihydroartemisinin and lumefantrine, were associated with multiple genetic polymorphisms in Plasmodium falciparum, and were lower in northern Uganda, where resistance-mediating mutations have emerged, compared to eastern Uganda.

    • Patrick K. Tumwebaze
    • , Melissa D. Conrad
    •  & Philip J. Rosenthal

  • Article
    | Open Access

    Plasmodium falciparum malaria is treated using artemisinin combination therapy (ACT), in which artemisinin is supplied along with partner drugs such as mefloquine, piperaquine, and lumefantrine. However, resistance has been reported in endemic regions. To identifying new effector genes involved in resistance, Iwanaga et al. develop a large scale transgenic screen with genomic libraries of resistance strains. Using this approach they provide evidence that transcriptional upregulation of pfmdr7 contributes to mefloquine resistance in a clinical isolate.

    • Shiroh Iwanaga
    • , Rie Kubota
    •  & Chairat Uthaipibull

  • Article
    | Open Access

    Toxoplasma gondii can infect all warm-blooded animals, with felidae being the definitive hosts. Despite this broad host range, most clinical and animal isolates belong to few clonal lineages. Here, Galal et al. perform whole-genome sequencing of isolates from distinct geographical regions and estimate T. gondii mutation rate and generation time. They find that recent waves of migration disseminated the parasite from Old to New World and identify a unique haplotype that likely accompanied the global expansion of cats and is today common to all intercontinental lineages and hybrid populations.

    • Lokman Galal
    • , Frédéric Ariey
    •  & Aurélien Mercier

  • Article
    | Open Access

    Progression of the canonical eukaryotic cell cycle is tightly regulated. While the cell cycle control of flagellated protozoa Trypanosoma brucei shares conserved features with other eukaryotes certain cell cycle checkpoints are absent. Here, Marques et al. provide a genome-scale RNAi screen followed by sorting of parasites according to their cell cycle stage to inform about cell cycle regulators of bloodstream T. brucei.

    • Catarina A. Marques
    • , Melanie Ridgway
    •  & David Horn

  • Article
    | Open Access

    The whipworm Trichuris trichiura is a soil-transmitted helminth that causes the neglected tropical disease trichuriasis in humans. Here, the authors produce whole genome sequences of modern and ancient samples from humans and non-human primates to characterise the genomic diversity and evolution of this pathogen.

    • Stephen R. Doyle
    • , Martin Jensen Søe
    •  & Christian Moliin Outzen Kapel

  • Article
    | Open Access

    Genetically identical cells can be phenotypically diverse to allow adaptive flexibility in a given environment. This phenotypic diversity is driven by epigenetic and transcriptional variability. Here, Tripathi et al. perform scRNA-seq of isogenic and non-isogenic Plasmodium falciparum schizont populations to explore transcriptional heterogeneity and stochastic gene expression during the course of development.

    • Jaishree Tripathi
    • , Lei Zhu
    •  & Zbynek Bozdech

  • Comment
    | Open Access

    Studying malaria transmission biology using scRNA-sequencing provides information on within-host strain diversity and transcriptional states. Here, we comment on our collaborative efforts at establishing single-cell capacities in sub-Saharan Africa and the challenges encountered in Mali’s endemic setting.

    • Antoine Dara
    • , Sunil Kumar Dogga
    •  & Mara K. N. Lawniczak

  • Article
    | Open Access

    Plasmodium malariae is a cause of malaria in humans and related species have been identified in non-human primates. Here, the authors use genomic analyses to establish that human P. malariae arose from a host switch of an ape parasite whilst a species infecting New World monkeys can be traced to a reverse zoonosis.

    • Lindsey J. Plenderleith
    • , Weimin Liu
    •  & Paul M. Sharp

  • Article
    | Open Access

    The snail Bulinus truncatus is an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium. Here the authors report the genome of Bu. truncatus, explore protein groups inferred to play a role in its interaction with the schistosome parasite, and identify expansions in gene families linked to immune response regulation.

    • Neil D. Young
    • , Andreas J. Stroehlein
    •  & Robin B. Gasser

  • Article
    | Open Access

    Schistosomiasis control strategies rely on mass drug administration (MDA) using praziquantel. Here, Berger et al. perform whole-genome sequencing of larvae from infected children across Ugandan regions with differing MDA histories. They find extensive gene flow with limited positive selection suggesting minimal change post MDA.

    • Duncan J. Berger
    • , Thomas Crellen
    •  & James A. Cotton

  • Article
    | Open Access

    Repeating fever is a hallmark of malaria. Here, a large-scale forward genetic screen in malaria-causing Plasmodium falciparum identifies genes associated with parasite tolerance to host fever, including apicoplast targeted isoprenoid biosynthesis—sharing features with artemisinin resistance.

    • Min Zhang
    • , Chengqi Wang
    •  & John H. Adams

  • Article
    | Open Access

    The control of the proper timing of emergence of apicomplexan parasite daughter cells during replication is crucial for their proliferation. Here, Khelifa et al. identify a key transcriptional regulator in the model Apicomplexa Toxoplasma gondii, which regulates the expression of transcription factors necessary for completion of the budding cycle.

    • Asma S. Khelifa
    • , Cecilia Guillen Sanchez
    •  & Mathieu Gissot

  • Article
    | Open Access

    Artemisinin (ART) resistance poses a problem for malaria elimination. Here, the authors perform genome-wide CRISPR screens in Toxoplasma gondii and identify that the putative transporter Tmem14c and mitochondrial heme metabolism, through mitochondrial protease DegP2, affect ART susceptibility.

    • Clare R. Harding
    • , Saima M. Sidik
    •  & Sebastian Lourido

  • Article
    | Open Access

    Metagenomics allows virus genome discovery, but the viral hosts are often not identified. Here, Kinsella et al. use recombination events between virus genomes, statistical association of viruses to hosts in clinical samples, and analysis of endogenous viral elements in host genomes to identify probable hosts of three CRESS virus families.

    • Cormac M. Kinsella
    • , Aldert Bart
    •  & Lia van der Hoek

  • Article
    | Open Access

    Many nematode worms, including Caenorhabditis elegans have XX/XO sex determination, while other species have XY. The authors use a new genome assembly of the filarial parasite Brugia malayi and published data to show that nematode sex chromosome evolution is highly plastic.

    • Jeremy M. Foster
    • , Alexandra Grote
    •  & Elodie Ghedin

  • Article
    | Open Access

    Histone modification and deposition are key regulators of transcription. Here, Kraus et al. provide a quantitative histone acetylome for Trypanosoma brucei, identify histone modifications enriched at transcription start sites, and show how H4 and H2A.Z acetylation affect histone deposition and transcription in trypanosomes.

    • Amelie J. Kraus
    • , Jens T. Vanselow
    •  & T. Nicolai Siegel

  • Article
    | Open Access

    Trypanosoma rely on variant surface glycoprotein (VSG) to escape host immunity, but mechanisms generating antigenic diversity of VSG are poorly understood. Here, Silva-Pereira et al. show that T. vivax has a limited antigenic repertoire compared to T. brucei and that recombination plays little role in diversifying T. vivax VSG sequences.

    • Sara Silva Pereira
    • , Kayo J. G. de Almeida Castilho Neto
    •  & Andrew P. Jackson

  • Article
    | Open Access

    Here, Bhattacharya et al. chemically mutagenize Leishmania and identify genes associated with resistance to miltefosine and paromomycin by next generation sequencing. The study shows that a protein kinase (CDPK1) can mediate resistance to paromomycin by affecting translation.

    • Arijit Bhattacharya
    • , Philippe Leprohon
    •  & Marc Ouellette

  • Article
    | Open Access

    Here, Nelson et al. use amplicon next-generation sequencing of two P. falciparum polymorphic gene regions to investigate the genetic similarity of parasite populations across time and space in a pediatric cohort in Kenya. They identify both micro- and macro-scale structuring of malaria parasites in this high-transmission setting, which could inform future intervention strategies.

    • Cody S. Nelson
    • , Kelsey M. Sumner
    •  & Wendy P. O’Meara

  • Article
    | Open Access

    Here, Llewellyn and colleagues present evidence of meiotic sex in Trypanosoma cruzi, the causative agent of Chagas disease. These findings have implications for the epidemiology of the disease in endemic regions and challenge existing ideas that the parasites are strictly clonal.

    • Philipp Schwabl
    • , Hideo Imamura
    •  & Martin S. Llewellyn

  • Article
    | Open Access

    Understanding genomic variation in Plasmodium falciparum parasites and inferring migration patterns can guide malaria elimination strategies. Using genome-wide data for 1722 parasites collected from 54 districts, the authors use identity-by-descent approaches to estimate regional parasite migration and spread of artemisinin drug resistance.

    • Amol C. Shetty
    • , Christopher G. Jacob
    •  & Marie A. Onyamboko

  • Article
    | Open Access

    Increasing resistance of Plasmodium falciparum strains to piperaquine (PPQ) in Southeast Asia is of concern and resistance mechanisms are incompletely understood. Here, Ross et al. show that mutations in the P. falciparum chloroquine resistance transporter are rapidly increasing in prevalence in Cambodia and confer resistance to PPQ.

    • Leila S. Ross
    • , Satish K. Dhingra
    •  & David A. Fidock

  • Article
    | Open Access

    Plasmodium vivax incidence in Malaysia has declined markedly over the last decade, despite evidence of chloroquine resistance. Here, Auburn et al. compare population structure of P. vivax in Malaysia to regions with intermediate and high transmission and identify genetic regions under putative selection.

    • Sarah Auburn
    • , Ernest D. Benavente
    •  & Ric N. Price

  • Article
    | Open Access

    African apes harbour six Plasmodium species, one of which gave rise to the human malaria parasite. Here, Sundaraman et al. use selective whole-genome amplification to determine genome sequences from two chimpanzee Plasmodiumspecies, shedding light on the evolutionary origin of the human parasite.

    • Sesh A. Sundararaman
    • , Lindsey J. Plenderleith
    •  & Beatrice H. Hahn

  • Article
    | Open Access

    The Asian liver fluke is a parasitic worm that is linked to an increased risk of malignant cancer. Here, the authors sequence the draft genome and transcriptome of this fluke and provide insight into how the species has adapted to be able to survive in the bile duct.

    • Neil D. Young
    • , Niranjan Nagarajan
    •  & Robin B. Gasser

  • Article
    | Open Access

    Tracing the source of malarial infections is an important step towards monitoring and controlling the disease. Here, Preston et al. analyse sequence data from 711 isolates and design a genetic barcode based on combined mitochondrial and apicoplast genomes that is able to distinguish between malaria parasites isolated from different geographical regions.

    • Mark D. Preston
    • , Susana Campino
    •  & Taane G. Clark

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