Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis

Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%–61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize α-glucans rather than β-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.

[1]  M. Mohebali,et al.  Inter- and intra-subtype variation of Blastocystis subtypes isolated from diarrheic and non-diarrheic patients in Iran. , 2017, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[2]  S. Al-Harthi,et al.  Subtyping of Blastocystis sp. isolated from symptomatic and asymptomatic individuals in Makkah, Saudi Arabia , 2017, Parasites & Vectors.

[3]  A. Roger,et al.  Lateral Gene Transfer in the Adaptation of the Anaerobic Parasite Blastocystis to the Gut , 2017, Current Biology.

[4]  T. Imir,et al.  Epidemiology and Prevalence of Blastocystis spp. in North Cyprus. , 2017, The American journal of tropical medicine and hygiene.

[5]  C. Clark,et al.  Current status of Blastocystis: A personal view. , 2016, Parasitology international.

[6]  K. Tan,et al.  Pathogenic mechanisms in Blastocystis spp. - Interpreting results from in vitro and in vivo studies. , 2016, Parasitology international.

[7]  Y. Koyama,et al.  Blastocystis phylogeny among various isolates from humans to insects. , 2016, Parasitology international.

[8]  M. Stanhope,et al.  Blastocystis Mitochondrial Genomes Appear to Show Multiple Independent Gains and Losses of Start and Stop Codons , 2016, Genome biology and evolution.

[9]  D. Fasshauer,et al.  Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell , 2016, BMC Evolutionary Biology.

[10]  E. Viscogliosi,et al.  On Blastocystis secreted cysteine proteases: a legumain-activated cathepsin B increases paracellular permeability of intestinal Caco-2 cell monolayers , 2016, Parasitology.

[11]  T. Gabaldón,et al.  Peroxisomes in parasitic protists. , 2016, Molecular and biochemical parasitology.

[12]  R. Traub,et al.  Comparison of faecal microbiota in Blastocystis-positive and Blastocystis-negative irritable bowel syndrome patients , 2016, Microbiome.

[13]  G. McFadden,et al.  Plasmodium falciparum Rab1A Localizes to Rhoptries in Schizonts , 2016, PloS one.

[14]  Harald R. Gruber-Vodicka,et al.  Environmental Breviatea harbor mutualistic Arcobacter epibionts , 2016, Nature.

[15]  G. Even,et al.  Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota , 2016, Scientific Reports.

[16]  Hui Lin,et al.  The Apoptotic Effect of Ursolic Acid on SK-Hep-1 Cells is Regulated by the PI3K/Akt, p38 and JNK MAPK Signaling Pathways , 2016, Molecules.

[17]  C. Brun,et al.  The TopoVIB-Like protein family is required for meiotic DNA double-strand break formation , 2016, Science.

[18]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[19]  A. Roger,et al.  Diversity and origins of anaerobic metabolism in mitochondria and related organelles , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[20]  H. Nielsen,et al.  A retrospective metagenomics approach to studying Blastocystis. , 2015, FEMS microbiology ecology.

[21]  K. Tan,et al.  Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1 , 2015, Genomics data.

[22]  Sushama Sivakumar,et al.  Spatiotemporal regulation of the anaphase-promoting complex in mitosis , 2015, Nature Reviews Molecular Cell Biology.

[23]  A. Kastaniotis,et al.  Expression and Evolution of the Non-Canonically Translated Yeast Mitochondrial Acetyl-CoA Carboxylase Hfa1p , 2014, PloS one.

[24]  M. Dapoigny,et al.  Blastocystis Is Associated with Decrease of Fecal Microbiota Protective Bacteria: Comparative Analysis between Patients with Irritable Bowel Syndrome and Control Subjects , 2014, PloS one.

[25]  Mark C. Field,et al.  Missing pieces of an ancient puzzle: evolution of the eukaryotic membrane-trafficking system. , 2014, Cold Spring Harbor perspectives in biology.

[26]  W. D. de Vos,et al.  The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. , 2014, FEMS microbiology ecology.

[27]  D. Barford,et al.  Molecular architecture and mechanism of the anaphase-promoting complex , 2014, Nature.

[28]  A. Roger,et al.  A Large Number of Nuclear Genes in the Human Parasite Blastocystis Require mRNA Polyadenylation to Create Functional Termination Codons , 2014, Genome biology and evolution.

[29]  Shohei Yamaoka,et al.  The mitochondrial Ras-related GTPase Miro: views from inside and outside the metazoan kingdom , 2014, Front. Plant Sci..

[30]  J. Ramshaw,et al.  Bacterial collagen-like proteins that form triple-helical structures. , 2014, Journal of structural biology.

[31]  D. Stark,et al.  Update on the pathogenic potential and treatment options for Blastocystis sp , 2014, Gut Pathogens.

[32]  K. Tan,et al.  Intra-Subtype Variation in Enteroadhesion Accounts for Differences in Epithelial Barrier Disruption and Is Associated with Metronidazole Resistance in Blastocystis Subtype-7 , 2014, PLoS neglected tropical diseases.

[33]  Feng Gao,et al.  Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method , 2014, Current genomics.

[34]  Sarah R. Smith,et al.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing , 2014, PLoS biology.

[35]  Neil D. Rawlings,et al.  MEROPS: the database of proteolytic enzymes, their substrates and inhibitors , 2013, Nucleic Acids Res..

[36]  Kazutaka Katoh,et al.  MAFFT: iterative refinement and additional methods. , 2014, Methods in molecular biology.

[37]  P. Scanlan,et al.  Blastocystis: getting to grips with our guileful guest. , 2013, Trends in parasitology.

[38]  C. Texier,et al.  Blastocystis, an unrecognized parasite: an overview of pathogenesis and diagnosis , 2013, Therapeutic advances in infectious disease.

[39]  Sean R. Eddy,et al.  Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..

[40]  S. Sugano,et al.  Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure , 2013, Current Biology.

[41]  D. Roos,et al.  Cryptic organelle homology in apicomplexan parasites: insights from evolutionary cell biology. , 2013, Current opinion in microbiology.

[42]  Sean R. Eddy,et al.  nhmmer: DNA homology search with profile HMMs , 2013, Bioinform..

[43]  B. Henrissat,et al.  Genome of the red alga Porphyridium purpureum , 2013, Nature Communications.

[44]  C. Clark,et al.  Variable geographic distribution of Blastocystis subtypes and its potential implications. , 2013, Acta tropica.

[45]  Christopher J. Tonkin,et al.  An Overexpression Screen of Toxoplasma gondii Rab-GTPases Reveals Distinct Transport Routes to the Micronemes , 2013, PLoS pathogens.

[46]  D. Nelson,et al.  The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[47]  M. Benchimol,et al.  The TvLEGU-1, a Legumain-Like Cysteine Proteinase, Plays a Key Role in Trichomonas vaginalis Cytoadherence , 2013, BioMed research international.

[48]  M. Frilander,et al.  The significant other: splicing by the minor spliceosome , 2012, Wiley interdisciplinary reviews. RNA.

[49]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[50]  Simon Hawkins,et al.  The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. , 2012, The Plant journal : for cell and molecular biology.

[51]  W. Martin,et al.  Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes , 2012, Microbiology and Molecular Reviews.

[52]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[53]  Alan J. Robinson,et al.  MitoMiner: a data warehouse for mitochondrial proteomics data , 2011, Nucleic Acids Res..

[54]  Y. Saeys,et al.  GenomeView: a next-generation genome browser , 2011, Nucleic acids research.

[55]  R. Feyereisen Insect CYP Genes and P450 Enzymes , 2012 .

[56]  D. A. Gomes,et al.  Stem cells and calcium signaling. , 2012, Advances in experimental medicine and biology.

[57]  Sébastien Tempel Using and understanding RepeatMasker. , 2012, Methods in molecular biology.

[58]  Liran Carmel,et al.  Origin and evolution of spliceosomal introns , 2012, Biology Direct.

[59]  M. E. Hodges,et al.  Conservation of ciliary proteins in plants with no cilia , 2011, BMC Plant Biology.

[60]  Pawel Herzyk,et al.  Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. , 2011, Genome research.

[61]  D. Moreira,et al.  The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes , 2011, BMC Evolutionary Biology.

[62]  U. Maier,et al.  A Single Peroxisomal Targeting Signal Mediates Matrix Protein Import in Diatoms , 2011, PloS one.

[63]  K. Na-Bangchang,et al.  Confutation of the existence of sequence-conserved cytochrome P450 enzymes in Plasmodium falciparum. , 2011, Acta tropica.

[64]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[65]  M. Eliáš,et al.  The Ras related GTPase Miro is not required for mitochondrial transport in Dictyostelium discoideum. , 2011, European journal of cell biology.

[66]  Florent E. Angly,et al.  Next Generation Sequence Assembly with AMOS , 2011, Current protocols in bioinformatics.

[67]  S. Ball,et al.  The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis. , 2011, Journal of experimental botany.

[68]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[69]  S. Raimondi,et al.  Folate Production by Probiotic Bacteria , 2011, Nutrients.

[70]  Narmada Thanki,et al.  CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..

[71]  J. Poulain,et al.  Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite , 2011, Genome Biology.

[72]  M. Yandell,et al.  Characterization of the Conus bullatus genome and its venom-duct transcriptome , 2011, BMC Genomics.

[73]  François Laviolette,et al.  Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies , 2010, J. Comput. Biol..

[74]  Oscar Franzén,et al.  Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate , 2010, BMC Genomics.

[75]  T. Tonon,et al.  Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes. , 2010, The New phytologist.

[76]  M. Ares,et al.  Purification of RNA using TRIzol (TRI reagent). , 2010, Cold Spring Harbor protocols.

[77]  Kresimir Josic,et al.  Comparative testing of DNA segmentation algorithms using benchmark simulations. , 2010, Molecular biology and evolution.

[78]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[79]  T. Gabaldón Peroxisome diversity and evolution , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[80]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[81]  Eileen Kraemer,et al.  EuPathDB: a portal to eukaryotic pathogen databases , 2009, Nucleic Acids Res..

[82]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[83]  Jürgen Pleiss,et al.  The Cytochrome P450 Engineering Database: integration of biochemical properties , 2009, BMC Biochemistry.

[84]  Sean R Eddy,et al.  A new generation of homology search tools based on probabilistic inference. , 2009, Genome informatics. International Conference on Genome Informatics.

[85]  Nicolas Lartillot,et al.  PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating , 2009, Bioinform..

[86]  N. Patron,et al.  The RAB Family GTPase Rab1A from Plasmodium falciparum Defines a Unique Paralog Shared by Chromalveolates and Rhizaria , 2009, The Journal of eukaryotic microbiology.

[87]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[88]  D. Moreira,et al.  A Complex Cell Division Machinery Was Present in the Last Common Ancestor of Eukaryotes , 2009, PloS one.

[89]  Fred D. Mast,et al.  Endoplasmic Reticulum-Associated Secretory Proteins Sec20p, Sec39p, and Dsl1p Are Involved in Peroxisome Biogenesis , 2009, Eukaryotic Cell.

[90]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[91]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[92]  D. Keene,et al.  Identification of the First Prokaryotic Collagen Sequence Motif That Mediates Binding to Human Collagen Receptors, Integrins α2β1 and α11β1* , 2008, Journal of Biological Chemistry.

[93]  P. Wincker,et al.  Complete circular DNA in the mitochondria-like organelles of Blastocystis hominis. , 2008, International Journal of Parasitology.

[94]  V. Pérez-Brocal,et al.  Analysis of Two Genomes from the Mitochondrion-Like Organelle of the Intestinal Parasite Blastocystis: Complete Sequences, Gene Content, and Genome Organization , 2008, Molecular biology and evolution.

[95]  K. Tan,et al.  Biochemical characterization of a mitochondrial-like organelle from Blastocystis sp. subtype 7. , 2008, Microbiology.

[96]  T. Mitchell,et al.  PclA, a pneumococcal collagen-like protein with selected strain distribution, contributes to adherence and invasion of host cells. , 2008, FEMS microbiology letters.

[97]  O. Gascuel,et al.  An improved general amino acid replacement matrix. , 2008, Molecular biology and evolution.

[98]  D. Posada jModelTest: phylogenetic model averaging. , 2008, Molecular biology and evolution.

[99]  S. Urban,et al.  An Entamoeba histolytica rhomboid protease with atypical specificity cleaves a surface lectin involved in phagocytosis and immune evasion. , 2008, Genes & development.

[100]  Sean R. Eddy,et al.  A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation , 2008, PLoS Comput. Biol..

[101]  M. Paul,et al.  Trehalose metabolism and signaling. , 2008, Annual review of plant biology.

[102]  A. Roger,et al.  Supplemental Data Organelles in Blastocystis That Blur the Distinction between Mitochondria and Hydrogenosomes , 2022 .

[103]  J. Logsdon,et al.  An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis , 2008, PloS one.

[104]  M. Puthia,et al.  Blastocystis ratti Contains Cysteine Proteases That Mediate Interleukin-8 Response from Human Intestinal Epithelial Cells in an NF-κB-Dependent Manner , 2007, Eukaryotic Cell.

[105]  Jürgen Pleiss,et al.  The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family , 2007, Bioinform..

[106]  K. Nito,et al.  Functional classification of Arabidopsis peroxisome biogenesis factors proposed from analyses of knockdown mutants. , 2007, Plant & cell physiology.

[107]  Paul Horton,et al.  Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .

[108]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[109]  C. Nombela,et al.  MAP kinase pathways as regulators of fungal virulence. , 2007, Trends in microbiology.

[110]  Ajit Varki,et al.  Siglecs and their roles in the immune system , 2007, Nature Reviews Immunology.

[111]  S. Müller,et al.  Vitamin and cofactor biosynthesis pathways in Plasmodium and other apicomplexan parasites. , 2007, Trends in parasitology.

[112]  Richard D. Hayes,et al.  Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis , 2007, Science.

[113]  S. Urban,et al.  Two Plasmodium Rhomboid Proteases Preferentially Cleave Different Adhesins Implicated in All Invasive Stages of Malaria , 2006, PLoS pathogens.

[114]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[115]  Burkhard Morgenstern,et al.  Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.

[116]  M. Puthia,et al.  Degradation of human secretory immunoglobulin A by Blastocystis , 2005, Parasitology Research.

[117]  I. Anderson,et al.  Entamoeba histolytica: observations on metabolism based on the genome sequence. , 2005, Experimental parasitology.

[118]  L. Sibley,et al.  A spatially localized rhomboid protease cleaves cell surface adhesins essential for invasion by Toxoplasma. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[119]  M. Sogin,et al.  Molecular Phylogenies of Blastocystis Isolates from Different Hosts: Implications for Genetic Diversity, Identification of Species, and Zoonosis , 2005, Journal of Clinical Microbiology.

[120]  Nicholas H. Putnam,et al.  The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism , 2004, Science.

[121]  James Alexander,et al.  Cysteine peptidases as virulence factors of Leishmania. , 2004, Current opinion in microbiology.

[122]  T. Wetter,et al.  Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. , 2004, Genome research.

[123]  Henning Urlaub,et al.  The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. , 2004, RNA.

[124]  A. Krogh,et al.  A combined transmembrane topology and signal peptide prediction method. , 2004, Journal of molecular biology.

[125]  F. Eisenhaber,et al.  A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. , 2004, Journal of molecular biology.

[126]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[127]  J. Bonifacino,et al.  The Mechanisms of Vesicle Budding and Fusion , 2004, Cell.

[128]  R. Parish,et al.  Histochemical and biochemical evidence for the presence of microbodies in Phytophthora palmivora , 1975, Archives of Microbiology.

[129]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[130]  G. Blobel,et al.  Structural Basis for the Function of the β Subunit of the Eukaryotic Signal Recognition Particle Receptor , 2003, Cell.

[131]  R. Chakrabarti,et al.  Potential Involvement of Extracellular Signal-regulated Kinase 1 and 2 in Encystation of a Primitive Eukaryote, Giardia lamblia , 2003, The Journal of Biological Chemistry.

[132]  E. Yap,et al.  Freeze-Fracture and Cytochemical Studies on the in Vitro Cyst Form of Reptilian Blastocystis pythoni , 2003, The Journal of eukaryotic microbiology.

[133]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[134]  T. Hunter,et al.  Evolution of protein kinase signaling from yeast to man. , 2002, Trends in biochemical sciences.

[135]  J Wade Harper,et al.  The anaphase-promoting complex: it's not just for mitosis any more. , 2002, Genes & development.

[136]  P. Sylvestre,et al.  A collagen‐like surface glycoprotein is a structural component of the Bacillus anthracis exosporium , 2002, Molecular microbiology.

[137]  M. Sajid,et al.  Cysteine proteases of parasitic organisms. , 2002, Molecular and biochemical parasitology.

[138]  D. Goldberg,et al.  Biological roles of proteases in parasitic protozoa. , 2002, Annual review of biochemistry.

[139]  Peer Bork,et al.  Recent improvements to the SMART domain-based sequence annotation resource , 2002, Nucleic Acids Res..

[140]  W. Martin,et al.  Pyruvate : NADP+ oxidoreductase from the mitochondrion of Euglena gracilis and from the apicomplexan Cryptosporidium parvum: a biochemical relic linking pyruvate metabolism in mitochondriate and amitochondriate protists. , 2001, Molecular biology and evolution.

[141]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[142]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[143]  V. Zaman,et al.  Scanning electron microscopy of the surface coat of Blastocystis hominis , 1999, Parasitology Research.

[144]  S. W. Tan,et al.  In vitro encystation and excystation of Blastocystis ratti , 1999, Parasitology.

[145]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[146]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[147]  Ching C. Wang,et al.  Interferon-γ Activation of a Mitogen-activated Protein Kinase, KFR1, in the Bloodstream Form of Trypanosoma brucei * , 1997, The Journal of Biological Chemistry.

[148]  V. Zaman Phase-contrast microscopy of cell division in Blastocystis hominis. , 1997, Annals of tropical medicine and parasitology.

[149]  P Vincens,et al.  Computational method to predict mitochondrially imported proteins and their targeting sequences. , 1996, European journal of biochemistry.

[150]  R. Borrás,et al.  Identification of surface coat carbohydrates in Blastocystis hominis by lectin probes. , 1996, International journal for parasitology.

[151]  V. Zaman,et al.  Ultrastructure of Blastocystis hominis cysts. , 1995, Parasitology research.

[152]  S. Furlong Sterols of parasitic protozoa and helminths. , 1989, Experimental parasitology.

[153]  P. Manning,et al.  Biochemistry and metabolism of Giardia. , 1989, The Journal of Protozoology.

[154]  P. Boreham,et al.  Ultrastructural variation of Blastocystis hominis stocks in culture. , 1989, International journal for parasitology.

[155]  C. Zierdt,et al.  Biochemical and ultrastructural study of Blastocystis hominis , 1988, Journal of clinical microbiology.

[156]  J. Doyle,et al.  A rapid DNA isolation procedure for small amounts of fresh leaf tissue , 1987 .

[157]  E. Pahlich,et al.  A rapid DNA isolation procedure for small quantities of fresh leaf tissue , 1980 .