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  • 1
    Article
    Article
    In: Nature Reviews Microbiology, 2011, Vol.9(9), p.633
    Description: This month's Genome Watch describes the impact of next-generation sequencing on the 'real-time' analysis of pathogen genomes during outbreaks.
    Keywords: Disease Outbreaks–Genetics ; Escherichia Coli–Instrumentation ; Genome, Bacterial–Methods ; Humans–Genetics ; Sequence Analysis, DNA–Genetics ; Sequence Analysis, DNA–Genetics ; Vibrio Cholerae–Genetics;
    ISSN: 1740-1526
    E-ISSN: 17401534
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 28 February 2012, Vol.109(9), pp.3416-21
    Description: Antigenic variation enables pathogens to avoid the host immune response by continual switching of surface proteins. The protozoan blood parasite Trypanosoma brucei causes human African trypanosomiasis ("sleeping sickness") across sub-Saharan Africa and is a model system for antigenic variation, surviving by periodically replacing a monolayer of variant surface glycoproteins (VSG) that covers its cell surface. We compared the genome of Trypanosoma brucei with two closely related parasites Trypanosoma congolense and Trypanosoma vivax, to reveal how the variant antigen repertoire has evolved and how it might affect contemporary antigenic diversity. We reconstruct VSG diversification showing that Trypanosoma congolense uses variant antigens derived from multiple ancestral VSG lineages, whereas in Trypanosoma brucei VSG have recent origins, and ancestral gene lineages have been repeatedly co-opted to novel functions. These historical differences are reflected in fundamental differences between species in the scale and mechanism of recombination. Using phylogenetic incompatibility as a metric for genetic exchange, we show that the frequency of recombination is comparable between Trypanosoma congolense and Trypanosoma brucei but is much lower in Trypanosoma vivax. Furthermore, in showing that the C-terminal domain of Trypanosoma brucei VSG plays a crucial role in facilitating exchange, we reveal substantial species differences in the mechanism of VSG diversification. Our results demonstrate how past VSG evolution indirectly determines the ability of contemporary parasites to generate novel variant antigens through recombination and suggest that the current model for antigenic variation in Trypanosoma brucei is only one means by which these parasites maintain chronic infections.
    Keywords: Evolution, Molecular ; Genome, Protozoan ; Antigenic Variation -- Genetics ; Immune Evasion -- Genetics ; Trypanosoma Brucei Brucei -- Immunology ; Trypanosoma Congolense -- Immunology ; Trypanosoma Vivax -- Immunology ; Variant Surface Glycoproteins, Trypanosoma -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 3
    Language: English
    In: Nucleic acids research, May 2011, Vol.39(9), pp.e57
    Description: Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net.
    Keywords: Software ; Genomics -- Methods ; Molecular Sequence Annotation -- Methods
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 4
    Language: English
    In: Science (New York, N.Y.), 04 May 2018, Vol.360(6388)
    Description: Severe malaria is caused by the apicomplexan parasite Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro. These essential genes are associated with drug resistance, represent leading vaccine candidates, and include approximately 1000 -conserved genes of unknown function. We validated this approach by testing proteasome pathways for individual mutants associated with artemisinin sensitivity.
    Keywords: Genes, Protozoan ; Malaria, Falciparum -- Parasitology ; Plasmodium Falciparum -- Genetics ; Reproduction, Asexual -- Genetics
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 5
    Language: English
    In: Nature, November 2018, Vol.563(7729), pp.121-125
    Description: Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses-Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing-that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
    Keywords: Antigenic Variation -- Genetics ; Chromatin -- Genetics ; DNA, Protozoan -- Metabolism ; Genome -- Genetics ; Trypanosoma Brucei Brucei -- Genetics
    ISSN: 00280836
    E-ISSN: 1476-4687
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  • 6
    In: Nature, 2014, Vol.507(7491), p.253
    Description: Commitment to and completion of sexual development are essential for malaria parasites (protists of the genus Plasmodium) to be transmitted through mosquitoes. The molecular mechanism(s) responsible for commitment have been hit her to unknown. Here we show that PbAP2-G, a conserved member of the apicomplexan AP2 (ApiAP2) family of DNA-binding proteins, is essential for the commitment of asexually replicating forms to sexual development in Plasmodium berghei, a malaria parasite of rodents. PbAP2-G was identified from mutations in its encoding gene, PBANKA_143750, which account for the loss of sexual development frequently observed in parasites transmitted artificially by blood passage. Systematic gene deletion of conserved ApiAP2 genes in Plasmodium confirmed the role of PbAP2-GandrevealedasecondApiAP2 member (PBANKA_103430, here termed PbAP2-G2) that significantly modulates but does not abolish gametocytogenesis, indicating that a cascade of ApiAP2 proteins are involved in commitment to the production and maturation of gametocytes. The data suggest a mechanism of commitment to gametocytogenesis in Plasmodium consistent with a positive feed- back loop involving PbAP2-G that could be exploited to prevent the transmission of this pernicious parasite. [PUBLICATION ]
    Keywords: Animals–Parasitology ; Culicidae–Deficiency ; DNA-Binding Proteins–Genetics ; DNA-Binding Proteins–Metabolism ; DNA-Binding Proteins–Cytology ; Feedback, Physiological–Growth & Development ; Female–Metabolism ; Gene Expression Regulation–Parasitology ; Germ Cells–Genetics ; Germ Cells–Cytology ; Germ Cells–Genetics ; Malaria–Physiology ; Male–Genetics ; Mutation–Metabolism ; Plasmodium Berghei–Genetics ; Plasmodium Berghei–Genetics ; Plasmodium Berghei–Genetics ; Protein Transport–Genetics ; Protozoan Proteins–Genetics ; Protozoan Proteins–Genetics ; Reproduction, Asexual–Genetics ; Sexual Development–Genetics ; Transcription, Genetic–Genetics ; Mutation ; Parasites ; Mosquitoes ; Proteins ; Flow Cytometry ; Epigenetics ; Deoxyribonucleic Acid–DNA ; Genomes ; Gene Expression ; Transcription Factors ; DNA-Binding Proteins ; Protozoan Proteins;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 7
    Article
    Article
    In: Nature Reviews Microbiology, 2010, Vol.8(10), p.681
    Description: This month's Genome Watch discusses ways to automatically produce 'base-perfect' genome sequences.
    Keywords: Genome–Genetics ; Sequence Analysis, DNA–Methods ; Sequence Analysis, DNA–Standards;
    ISSN: 1740-1526
    E-ISSN: 17401534
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  • 8
    Language: English
    In: Journal of Bacteriology, 2011, Vol. 193(19), p.5600
    Description: Mycobacterium bovis bacillus Calmette-Guerin (BCG) is the only vaccine available against tuberculosis, and the strains used worldwide represent a family of daughter strains with distinct genotypic characteristics. Here we report the complete genome sequence of M. bovis BCG Moreau, the strain in continuous use in Brazil for vaccine production since the 1920s. doi: 10.1128/JB.05827-11
    Keywords: Bcg -- Health Aspects ; Mycobacterium Tuberculosis -- Genetic Aspects ; Mycobacterium Tuberculosis -- Health Aspects ; Mycobacterium Tuberculosis -- Research ; Tuberculosis -- Causes Of ; Tuberculosis -- Prevention ; Tuberculosis -- Research;
    ISSN: 1098-5530
    ISSN: 10985530
    ISSN: 00219193
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  • 9
    Language: English
    In: Nucleic acids research, 08 July 2016, Vol.44(W1), pp.W29-34
    Description: Currently available sequencing technologies enable quick and economical sequencing of many new eukaryotic parasite (apicomplexan or kinetoplastid) species or strains. Compared to SNP calling approaches, de novo assembly of these genomes enables researchers to additionally determine insertion, deletion and recombination events as well as to detect complex sequence diversity, such as that seen in variable multigene families. However, there currently are no automated eukaryotic annotation pipelines offering the required range of results to facilitate such analyses. A suitable pipeline needs to perform evidence-supported gene finding as well as functional annotation and pseudogene detection up to the generation of output ready to be submitted to a public database. Moreover, no current tool includes quick yet informative comparative analyses and a first pass visualization of both annotation and analysis results. To overcome those needs we have developed the Companion web server (http://companion.sanger.ac.uk) providing parasite genome annotation as a service using a reference-based approach. We demonstrate the use and performance of Companion by annotating two Leishmania and Plasmodium genomes as typical parasite cases and evaluate the results compared to manually annotated references.
    Keywords: Genome, Protozoan ; Software ; Leishmania -- Genetics ; Plasmodium Falciparum -- Genetics ; Protozoan Proteins -- Genetics ; RNA, Protozoan -- Genetics
    E-ISSN: 1362-4962
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  • 10
    Language: English
    In: Nucleic acids research, 28 February 2017, Vol.45(4), pp.1889-1901
    Description: For reasons that remain unknown, the Plasmodium falciparum genome has an exceptionally high AT content compared to other Plasmodium species and eukaryotes in general - nearly 80% in coding regions and approaching 90% in non-coding regions. Here, we examine how this phenomenon relates to genome-wide patterns of de novo mutation. Mutation accumulation experiments were performed by sequential cloning of six P. falciparum isolates growing in human erythrocytes in vitro for 4 years, with 279 clones sampled for whole genome sequencing at different time points. Genome sequence analysis of these samples revealed a significant excess of G:C to A:T transitions compared to other types of nucleotide substitution, which would naturally cause AT content to equilibrate close to the level seen across the P. falciparum reference genome (80.6% AT). These data also uncover an extremely high rate of small indel mutation relative to other species, primarily associated with repetitive AT-rich sequences, in addition to larger-scale structural rearrangements focused in antigen-coding var genes. In conclusion, high AT content in P. falciparum is driven by a systematic mutational bias and ultimately leads to an unusual level of microstructural plasticity, raising the question of whether this contributes to adaptive evolution.
    Keywords: Base Composition ; Genome, Protozoan ; Mutation ; Plasmodium Falciparum -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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