Genomes and Genes
Summary: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.
- Kidgell C, Volkman S, Daily J, Borevitz J, Plouffe D, Zhou Y, et al. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog. 2006;2:e57 pubmed..We speculate that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs. ..
- Nagamune K, Sibley L. Comparative genomic and phylogenetic analyses of calcium ATPases and calcium-regulated proteins in the apicomplexa. Mol Biol Evol. 2006;23:1613-27 pubmed..The central importance of calcium in signaling and development, and the novel characteristics of many of these systems, indicates that parasite calcium pathways may be exploited as new therapeutic targets for intervention. ..
- Morrison H, McArthur A, Gillin F, Aley S, Adam R, Olsen G, et al. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science. 2007;317:1921-6 pubmed..This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite. ..
- Hirt R, Noel C, Sicheritz Ponten T, Tachezy J, Fiori P. Trichomonas vaginalis surface proteins: a view from the genome. Trends Parasitol. 2007;23:540-7 pubmed..Here, we review the existing data on T. vaginalis surface proteins and summarize some of the main findings from the recent in silico characterization of its candidate surface proteins. ..
- Hutchinson O, Picozzi K, Jones N, Mott H, Sharma R, Welburn S, et al. Variant Surface Glycoprotein gene repertoires in Trypanosoma brucei have diverged to become strain-specific. BMC Genomics. 2007;8:234 pubmed..A consequence of strain-specific VSG repertoires is that any vaccine based on large numbers of VSGs from a single strain will only provide partial protection against other strains. ..
- Felu C, Pasture J, Pays E, Perez Morga D. Diagnostic potential of a conserved genomic rearrangement in the Trypanosoma brucei gambiense-specific TGSGP locus. Am J Trop Med Hyg. 2007;76:922-9 pubmed..b. gambiense isolates. ..
- Fey P, Gaudet P, Pilcher K, Franke J, Chisholm R. dictyBase and the Dicty Stock Center. Methods Mol Biol. 2006;346:51-74 pubmed..Here we will describe how to navigate the website and mine the extensive database to help users make optimal use of this invaluable resource. ..
- Prabhu A, Morrison H, Martinez C, Adam R. Characterisation of the subtelomeric regions of Giardia lamblia genome isolate WBC6. Int J Parasitol. 2007;37:503-13 pubmed..These studies of the subtelomeric regions of Giardia may contribute to our understanding of the factors that maintain stability, while allowing diversity in chromosome structure. ..
- Arnaiz O, Cain S, Cohen J, Sperling L. ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res. 2007;35:D439-44 pubmed..Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community...
- Arner E, Kindlund E, Nilsson D, Farzana F, Ferella M, Tammi M, et al. Database of Trypanosoma cruzi repeated genes: 20,000 additional gene variants. BMC Genomics. 2007;8:391 pubmed..Five repetitive genes were studied in more detail, in order to illustrate how the database can be used to analyze and extract information about gene repeats with different characteristics in Trypanosoma cruzi. ..
- Zubacova Z, Cimburek Z, Tachezy J. Comparative analysis of trichomonad genome sizes and karyotypes. Mol Biochem Parasitol. 2008;161:49-54 pubmed publisher..The data presented here provide primary information towards selecting a trichomonad species for future large-scale sequencing to elucidate the evolution of unusual parabasalid genomes. ..
- Chakrabarti K, Pearson M, Grate L, Sterne Weiler T, Deans J, Donohue J, et al. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA. 2007;13:1923-39 pubmed..These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts. ..
- Aurrecoechea C, Brestelli J, Brunk B, Dommer J, Fischer S, Gajria B, et al. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2009;37:D539-43 pubmed publisher..Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis. ..
- Boyle J, Rajasekar B, Saeij J, Ajioka J, Berriman M, Paulsen I, et al. Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii. Proc Natl Acad Sci U S A. 2006;103:10514-10519 pubmed publisher..The simplicity of this family tree demonstrates that even a single cross can lead to the emergence and dominance of a new clonal genotype that completely alters the population biology of a sexual pathogen. ..
- Gunasekera A, Myrick A, Le Roch K, Winzeler E, Wirth D. Plasmodium falciparum: genome wide perturbations in transcript profiles among mixed stage cultures after chloroquine treatment. Exp Parasitol. 2007;117:87-92 pubmed..Molecular Microbiology 50, 1229-1239]. These findings are important to report, given the striking contrast to similar studies in other model eukaryotic organisms. ..
- Iengar P, Joshi N. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum. BMC Genomics. 2009;10:18 pubmed publisher..The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf. ..
- Cohen Freue G, Holzer T, Forney J, McMaster W. Global gene expression in Leishmania. Int J Parasitol. 2007;37:1077-86 pubmed
- Slamovits C, Saldarriaga J, Larocque A, Keeling P. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes. J Mol Biol. 2007;372:356-68 pubmed..Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes. ..
- Kulakova L, Singer S, Conrad J, Nash T. Epigenetic mechanisms are involved in the control of Giardia lamblia antigenic variation. Mol Microbiol. 2006;61:1533-42 pubmed..Lack of vsp rearrangements and acetylation of expressed immediate upstream regions implicates involvement of epigenetic mechanisms in antigenic variation. ..
- Picazarri K, Nakada Tsukui K, Nozaki T. Autophagy during proliferation and encystation in the protozoan parasite Entamoeba invadens. Infect Immun. 2008;76:278-88 pubmed..invadens. These results suggest that the core machinery for autophagy is conserved and plays an important role during proliferation and differentiation in Entamoeba. ..
- Teodorovic S, Walls C, Elmendorf H. Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome. Nucleic Acids Res. 2007;35:2544-53 pubmed..lamblia gives us insight into the interaction between transcriptional machinery and promoter elements, and may be the prominent source of the abundant antisense transcription in this parasite. ..
- Wakaguri H, Suzuki Y, Sasaki M, Sugano S, Watanabe J. Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs. BMC Genomics. 2009;10:312 pubmed publisher..To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites...
- Wilkinson S, Taylor M, Horn D, Kelly J, Cheeseman I. A mechanism for cross-resistance to nifurtimox and benznidazole in trypanosomes. Proc Natl Acad Sci U S A. 2008;105:5022-7 pubmed publisher..This potential for drug resistance by a simple mechanism has important implications, because nifurtimox is currently undergoing phase III clinical trials against African trypanosomiasis. ..
- Kamikawa R, Inagaki Y, Sako Y. Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria. Protist. 2007;158:239-45 pubmed..However, current sequence data on dinoflagellate mitochondria are insufficient to reject the alternative scenario, in which the rRNA fragmentation evolved independently in apicomplexan and dinoflagellate mitochondria. ..
- Andersson J, Sjögren A, Horner D, Murphy C, Dyal P, Svard S, et al. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics. 2007;8:51 pubmed..barkhanus)...
- Yee J, Tang A, Lau W, Ritter H, Delport D, Page M, et al. Core histone genes of Giardia intestinalis: genomic organization, promoter structure, and expression. BMC Mol Biol. 2007;8:26 pubmed..Our inability to locate a gene encoding the linker histone H1 leads us to speculate that the H1 protein may not be required for the compaction of Giardia's small and gene-rich genome. ..
- Clark C, Alsmark U, Tazreiter M, Saito Nakano Y, Ali V, Marion S, et al. Structure and content of the Entamoeba histolytica genome. Adv Parasitol. 2007;65:51-190 pubmed..In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes. ..
- Field M, Natesan S, Gabernet Castello C, Koumandou V. Intracellular trafficking in the trypanosomatids. Traffic. 2007;8:629-39 pubmed
- Tienda Luna I, Yin Y, Carrion M, Huang Y, Cai H, Sanchez M, et al. Inferring the skeleton cell cycle regulatory network of malaria parasite using comparative genomic and variational Bayesian approaches. Genetica. 2008;132:131-42 pubmed
- Jiang H, Yi M, Mu J, Zhang L, Ivens A, Klimczak L, et al. Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray. BMC Genomics. 2008;9:398 pubmed publisher..Our method for accurate mSFP detection and the mSFP identified will greatly facilitate large-scale studies of genome variation in the P. falciparum parasite and provide useful resources for mapping important parasite traits. ..
- Lu F, Jiang H, Ding J, Mu J, Valenzuela J, Ribeiro J, et al. cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics. 2007;8:255 pubmed..This study provides valuable information for genome annotation that will be critical for functional analyses. ..
- Jeffares D, Pain A, Berry A, Cox A, Stalker J, Ingle C, et al. Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet. 2007;39:120-5 pubmed..This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum. ..
- Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak T, Landweber L. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature. 2008;451:153-8 pubmed..Injection of artificial templates reprogrammes the DNA rearrangement pathway, suggesting that RNA molecules guide genome rearrangement...
- Jackson A, Vaughan S, Gull K. Evolution of tubulin gene arrays in Trypanosomatid parasites: genomic restructuring in Leishmania. BMC Genomics. 2006;7:261 pubmed..This fundamental reorganisation accounted for the dissimilar genomic architectures of T. brucei and L. major tubulin repertoires. ..
- Gallego E, Alvarado M, Wasserman M. Identification and expression of the protein ubiquitination system in Giardia intestinalis. Parasitol Res. 2007;101:1-7 pubmed..A constant ubiquitin expression persisted during the parasite's differentiation processes, whereas variation in transcription was observed in the other genes under study. ..
- Carlton J, Escalante A, Neafsey D, Volkman S. Comparative evolutionary genomics of human malaria parasites. Trends Parasitol. 2008;24:545-50 pubmed publisher..evolutionary genomics of the two species in the light of several presentations at the Molecular Approaches to Malaria 2008 meeting in Lorne, Australia and ask the question: can evolutionary genomics of one species inform the other? ..
- Vaughan A, Chiu S, Ramasamy G, Li L, Gardner M, Tarun A, et al. Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis. Bioinformatics. 2008;24:i383-9 pubmed publisher..The addition of newly annotated genes will facilitate the use of P. yoelii as a model system for studying human malaria. Supplementary data are available at Bioinformatics online. ..
- Hamilton E, Dear P, Rowland T, Saks K, Eisen J, Orias E. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics. 2006;88:443-51 pubmed
- Bringaud F, Ghedin E, El Sayed N, Papadopoulou B. Role of transposable elements in trypanosomatids. Microbes Infect. 2008;10:575-81 pubmed publisher..In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions. ..
- Franzén O, Jerlström Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner D, et al. Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?. PLoS Pathog. 2009;5:e1000560 pubmed publisher..01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species. ..
- Shock J, Fischer K, Derisi J. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biol. 2007;8:R134 pubmed..This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum. ..
- Ginsburg H. Progress in in silico functional genomics: the malaria Metabolic Pathways database. Trends Parasitol. 2006;22:238-40 pubmed..Additional features, such as links to other databases and the incorporation of transcriptomic clocks, are elucidated. Comparison of Metabolic Pathways to other similar databases is analyzed. ..