Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania

[1]  Mark C. Field,et al.  Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism , 2016, Current Biology.

[2]  J. Lukeš,et al.  New Approaches to Systematics of Trypanosomatidae: Criteria for Taxonomic (Re)description. , 2015, Trends in parasitology.

[3]  B. Lemaître,et al.  Infection Dynamics and Immune Response in a Newly Described Drosophila-Trypanosomatid Association , 2015, mBio.

[4]  F. Opperdoes,et al.  Leptomonas seymouri: Adaptations to the Dixenous Life Cycle Analyzed by Genome Sequencing, Transcriptome Profiling and Co-infection with Leishmania donovani , 2015, PLoS pathogens.

[5]  A. T. Vasconcelos,et al.  Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains , 2015, BMC Genomics.

[6]  Diego Miranda-Saavedra,et al.  Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites , 2015, eLife.

[7]  C. Cantacessi,et al.  The past, present, and future of Leishmania genomics and transcriptomics , 2015, Trends in parasitology.

[8]  J. Lukeš,et al.  Kentomonas gen. n., a new genus of endosymbiont-containing trypanosomatids of Strigomonadinae subfam. n. , 2014, Protist.

[9]  Mark J. Sistrom,et al.  Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex , 2014, Genome biology and evolution.

[10]  S. Kelly,et al.  SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes , 2014, Molecular and biochemical parasitology.

[11]  A. Jackson.  Genome evolution in trypanosomatid parasites , 2014, Parasitology.

[12]  G. McVean,et al.  Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications , 2014, Nature Genetics.

[13]  J. McKerrow,et al.  Determinants of disease phenotype in trypanosomatid parasites. , 2014, Trends in parasitology.

[14]  J. Lukeš,et al.  Evolution of parasitism in kinetoplastid flagellates. , 2014, Molecular and biochemical parasitology.

[15]  K. Hill,et al.  Motility and more: the flagellum of Trypanosoma brucei , 2014, Nature Reviews Microbiology.

[16]  R. Kay,et al.  Characterization of TSET, an ancient and widespread membrane trafficking complex , 2014, eLife.

[17]  J. Derisi,et al.  A Draft Genome of the Honey Bee Trypanosomatid Parasite Crithidia mellificae , 2014, PloS one.

[18]  M. Sieracki,et al.  The others: our biased perspective of eukaryotic genomes , 2014, Trends in ecology & evolution.

[19]  Mark C. Field,et al.  A comparative analysis of trypanosomatid SNARE proteins , 2014, Parasitology international.

[20]  Mark C. Field,et al.  The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants , 2014, PLoS genetics.

[21]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[22]  N. Dickens,et al.  Regulators of Trypanosoma brucei Cell Cycle Progression and Differentiation Identified Using a Kinome-Wide RNAi Screen , 2014, PLoS pathogens.

[23]  M. Berriman,et al.  Genomic Confirmation of Hybridisation and Recent Inbreeding in a Vector-Isolated Leishmania Population , 2014, PLoS genetics.

[24]  C. Jaffe,et al.  Identification of a Secreted Casein Kinase 1 in Leishmania donovani: Effect of Protein over Expression on Parasite Growth and Virulence , 2013, PloS one.

[25]  A. T. Vasconcelos,et al.  Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers , 2013, BMC Evolutionary Biology.

[26]  Peng Liu,et al.  An Optimal Test with Maximum Average Power While Controlling FDR with Application to RNA‐Seq Data , 2013, Biometrics.

[27]  Qiandong Zeng,et al.  Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily , 2013, Bioinform..

[28]  P. Mieczkowski,et al.  The Genome Sequence of Leishmania (Leishmania) amazonensis: Functional Annotation and Extended Analysis of Gene Models , 2013, DNA research : an international journal for rapid publication of reports on genes and genomes.

[29]  Eugene V Koonin,et al.  Genome reduction as the dominant mode of evolution , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[30]  F. Ayala,et al.  How clonal are Trypanosoma and Leishmania? , 2013, Trends in parasitology.

[31]  N. Grishin,et al.  Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. , 2013, Genes & development.

[32]  Allan Cézar de Azevedo Martins,et al.  Predicting the Proteins of Angomonas deanei, Strigomonas culicis and Their Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family , 2013, PloS one.

[33]  Mark C. Field,et al.  Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids , 2013, Molecular phylogenetics and evolution.

[34]  Mark C. Field,et al.  Proteomic Analysis of Clathrin Interactions in Trypanosomes Reveals Dynamic Evolution of Endocytosis , 2013, Traffic.

[35]  David M. A. Martin,et al.  Global Quantitative SILAC Phosphoproteomics Reveals Differential Phosphorylation Is Widespread between the Procyclic and Bloodstream Form Lifecycle Stages of Trypanosoma brucei , 2013, Journal of proteome research.

[36]  F. Alvarez-Valin,et al.  Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax , 2013, BMC Genomics.

[37]  S. Sundar,et al.  SOLiD™ Sequencing of Genomes of Clinical Isolates of Leishmania donovani from India Confirm Leptomonas Co-Infection and Raise Some Key Questions , 2013, PloS one.

[38]  P. Volf,et al.  Leishmania development in sand flies: parasite-vector interactions overview , 2012, Parasites & Vectors.

[39]  G. H. Coombs,et al.  Distinct Roles in Autophagy and Importance in Infectivity of the Two ATG4 Cysteine Peptidases of Leishmania major* , 2012, The Journal of Biological Chemistry.

[40]  P. Schmid-Hempel,et al.  Probing Mixed-Genotype Infections II: High Multiplicity in Natural Infections of the Trypanosomatid, Crithidia bombi, in Its Host, Bombus spp , 2012, PloS one.

[41]  J. Lukeš,et al.  New Species of Insect Trypanosomatids from Costa Rica and the Proposal for a New Subfamily within the Trypanosomatidae , 2012, The Journal of eukaryotic microbiology.

[42]  H. Michael G. Lattorff,et al.  Seasonal variability of prevalence and occurrence of multiple infections shape the population structure of Crithidia bombi, an intestinal parasite of bumblebees (Bombus spp.) , 2012, MicrobiologyOpen.

[43]  F. Ayala,et al.  Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa , 2012, Proceedings of the National Academy of Sciences.

[44]  Z. Cucunubá,et al.  Contemporary cryptic sexuality in Trypanosoma cruzi , 2012, Molecular ecology.

[45]  C. R. Alves,et al.  Proteinases as virulence factors in Leishmania spp. infection in mammals , 2012, Parasites & Vectors.

[46]  A. Horák,et al.  Cosmopolitan distribution of a trypanosomatid Leptomonas pyrrhocoris. , 2012, Protist.

[47]  P. Banerjee,et al.  Coinfection of Leptomonas seymouri and Leishmania donovani in Indian Leishmaniasis , 2012, Journal of Clinical Microbiology.

[48]  W. Gibson.  The origins of the trypanosome genome strains Trypanosoma brucei brucei TREU 927, T. b. gambiense DAL 972, T. vivax Y486 and T. congolense IL3000 , 2012, Parasites & Vectors.

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

[50]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[51]  N. El-Sayed,et al.  Functional genomics of trypanosomatids , 2012, Parasite immunology.

[52]  Matthew Berriman,et al.  Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data , 2011, Bioinform..

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

[54]  Mark C. Field,et al.  A Novel Rho-Like Protein TbRHP Is Involved in Spindle Formation and Mitosis in Trypanosomes , 2011, PloS one.

[55]  D. Sahlender,et al.  The Fifth Adaptor Protein Complex , 2011, PLoS biology.

[56]  J. Lukeš,et al.  Genomic Characterization of Neoparamoeba pemaquidensis (Amoebozoa) and Its Kinetoplastid Endosymbiont , 2011, Eukaryotic Cell.

[57]  P. Volf,et al.  Visualisation of Leishmania donovani Fluorescent Hybrids during Early Stage Development in the Sand Fly Vector , 2011, PloS one.

[58]  Mark C. Field,et al.  Evolutionary reconstruction of the retromer complex and its function in Trypanosoma brucei , 2011, Journal of Cell Science.

[59]  Alejandro E Leroux,et al.  Functional characterization of NADP-dependent isocitrate dehydrogenase isozymes from Trypanosoma cruzi. , 2011, Molecular and biochemical parasitology.

[60]  P. Schmid-Hempel,et al.  Genetic exchange and emergence of novel strains in directly transmitted trypanosomatids. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[61]  P. Bastien,et al.  FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major , 2011, Cellular microbiology.

[62]  R. Moreno-Sánchez,et al.  Targeting trypanothione metabolism in trypanosomatid human parasites. , 2010, Current drug targets.

[63]  José Osorio y Fortéa,et al.  Identification of Leishmania‐specific protein phosphorylation sites by LC‐ESI‐MS/MS and comparative genomics analyses , 2010, Proteomics.

[64]  B. Szöör.  Trypanosomatid protein phosphatases , 2010, Molecular and biochemical parasitology.

[65]  Miklós Csuös,et al.  Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood , 2010, Bioinform..

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

[67]  J. Lukeš,et al.  Two New Species of Trypanosomatid Parasites Isolated from Heteroptera in Costa Rica , 2010, The Journal of eukaryotic microbiology.

[68]  Mark Johnson,et al.  Is HAP2-GCS1 an ancestral gamete fusogen? , 2010, Trends in cell biology.

[69]  P. Volf,et al.  Leishmania major Glycosylation Mutants Require Phosphoglycans (lpg2 −) but Not Lipophosphoglycan (lpg1 −) for Survival in Permissive Sand Fly Vectors , 2010, PLoS neglected tropical diseases.

[70]  Eileen Kraemer,et al.  TriTrypDB: a functional genomic resource for the Trypanosomatidae , 2009, Nucleic Acids Res..

[71]  Mark C. Field,et al.  The trypanosome flagellar pocket , 2009, Nature Reviews Microbiology.

[72]  A. Jackson.  The Evolution of Amastin Surface Glycoproteins in Trypanosomatid Parasites , 2009, Molecular biology and evolution.

[73]  D. Dobson,et al.  Demonstration of Genetic Exchange During Cyclical Development of Leishmania in the Sand Fly Vector , 2009, Science.

[74]  G. H. Coombs,et al.  Characterization of unusual families of ATG8-like proteins and ATG12 in the protozoan parasite Leishmania major , 2009, Autophagy.

[75]  Mark C. Field,et al.  Evolution of the Multivesicular Body ESCRT Machinery; Retention Across the Eukaryotic Lineage , 2008, Traffic.

[76]  X. Zhong,et al.  A proposed role for Leishmania major carboxypeptidase in peptide catabolism. , 2008, Biochemical and biophysical research communications.

[77]  F. Bringaud,et al.  Role of transposable elements in trypanosomatids. , 2008, Microbes and infection.

[78]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[79]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[80]  Richard M. Clark,et al.  Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana , 2007, Science.

[81]  Brian White,et al.  Comparative genomic analysis of three Leishmania species that cause diverse human disease , 2007, Nature Genetics.

[82]  C. Ravel,et al.  Increased transmission potential of Leishmania major/Leishmania infantum hybrids. , 2007, International journal for parasitology.

[83]  P. T. Englund,et al.  A fatty-acid synthesis mechanism specialized for parasitism , 2007, Nature Reviews Microbiology.

[84]  Mark C. Field,et al.  Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins , 2007, BMC Evolutionary Biology.

[85]  Frédéric Bringaud,et al.  Metabolic functions of glycosomes in trypanosomatids. , 2006, Biochimica et biophysica acta.

[86]  C. Soderlund,et al.  SyMAP: A system for discovering and viewing syntenic regions of FPC maps. , 2006, Genome research.

[87]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[88]  U. Lopes,et al.  TcRho1, the Trypanosoma cruzi Rho homologue, regulates cell-adhesion properties: evidence for a conserved function. , 2006, Biochemical and biophysical research communications.

[89]  P. Volf,et al.  Virulent and attenuated lines of Leishmania major: DNA karyotypes and differences in metalloproteinase GP63. , 2006, Folia parasitologica.

[90]  C. Mandal,et al.  Glycobiology of Leishmania donovani. , 2006, The Indian journal of medical research.

[91]  F. Opperdoes,et al.  The extraordinary mitochondrion and unusual citric acid cycle in Trypanosoma brucei. , 2005, Biochemical Society transactions.

[92]  Mark C. Field.  Signalling the genome: the Ras-like small GTPase family of trypanosomatids. , 2005, Trends in parasitology.

[93]  M. Parsons,et al.  Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi , 2005, BMC Genomics.

[94]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[95]  David M. A. Martin,et al.  The Genome of the African Trypanosome Trypanosoma brucei , 2005, Science.

[96]  B. Haas,et al.  The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease , 2005, Science.

[97]  Heather J Munden,et al.  The Genome of the Kinetoplastid Parasite, Leishmania major , 2005, Science.

[98]  F. Opperdoes,et al.  New Functions for Parts of the Krebs Cycle in Procyclic Trypanosoma brucei, a Cycle Not Operating as a Cycle* , 2005, Journal of Biological Chemistry.

[99]  W. Wong,et al.  Bayes empirical bayes inference of amino acid sites under positive selection. , 2005, Molecular biology and evolution.

[100]  D. Goulding,et al.  Functional analysis of TbARL1, an N-myristoylated Golgi protein essential for viability in bloodstream trypanosomes , 2005, Journal of Cell Science.

[101]  C. Barillas-Mury,et al.  A Role for Insect Galectins in Parasite Survival , 2004, Cell.

[102]  D. Maslov,et al.  Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene , 2004, Parasitology.

[103]  B. Kolli,et al.  Down-regulation of gp63 in Leishmania amazonensis reduces its early development in Lutzomyia longipalpis. , 2004, Microbes and infection.

[104]  Samuel V. Angiuoli,et al.  Gene synteny and evolution of genome architecture in trypanosomatids. , 2004, Molecular and biochemical parasitology.

[105]  L. McAlister-Henn,et al.  Influence of compartmental localization on the function of yeast NADP+-specific isocitrate dehydrogenases. , 2004, Archives of biochemistry and biophysics.

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

[107]  Sean Thomas,et al.  Transcription in kinetoplastid protozoa: why be normal? , 2003, Microbes and infection.

[108]  G. H. Coombs,et al.  Cysteine Protease B of Leishmania mexicana Inhibits Host Th1 Responses and Protective Immunity 1 , 2003, The Journal of Immunology.

[109]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[110]  R. Nielsen,et al.  Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. , 2003, Genetics.

[111]  M. Ferreira,et al.  Some aspects of protozoan infections in immunocompromised patients- a review. , 2002, Memorias do Instituto Oswaldo Cruz.

[112]  W. McMaster,et al.  Targeted gene deletion in Leishmania major identifies leishmanolysin (GP63) as a virulence factor. , 2002, Molecular and biochemical parasitology.

[113]  P. Fearnhead,et al.  A coalescent-based method for detecting and estimating recombination from gene sequences. , 2002, Genetics.

[114]  M. Ouellette,et al.  Reduced Infectivity of a Leishmania donovani Biopterin Transporter Genetic Mutant and Its Use as an Attenuated Strain for Vaccination , 2002, Infection and Immunity.

[115]  J. Lukeš,et al.  Crithidia fasciculata: a test for genetic exchange. , 2001, Experimental parasitology.

[116]  S. Turco,et al.  Glycoconjugate structures of parasitic protozoa. , 2001, Glycobiology.

[117]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.

[118]  J. Cassuto,et al.  HIV and Leishmania coinfection: a review of 91 cases with focus on atypical locations of Leishmania. , 2000, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[119]  F. Pratlong,et al.  Leishmania, Trypanosoma and Monoxenous Trypanosomatids as Emerging Opportunistic Agents1 , 2000, The Journal of eukaryotic microbiology.

[120]  Y. Stierhof,et al.  Proteophosphoglycans of Leishmania mexicana. Identification, purification, structural and ultrastructural characterization of the secreted promastigote proteophosphoglycan pPPG2, a stage-specific glycoisoform of amastigote aPPG. , 1999, The Biochemical journal.

[121]  A. Frasch,et al.  The NADP+-linked glutamate dehydrogenase from Trypanosoma cruzi: sequence, genomic organization and expression. , 1998, The Biochemical journal.

[122]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[123]  J. Blum,et al.  D-lactate production by Leishmania braziliensis through the glyoxalase pathway. , 1988, Molecular and biochemical parasitology.

[124]  E. Gander,et al.  Morphologic and biochemical characterization of Crithidia brasiliensis sp. n. , 1980, The Journal of protozoology.

[125]  R. McGhee,et al.  Biology and physiology of the lower Trypanosomatidae , 1980, Microbiological reviews.

[126]  E. Kitajima,et al.  Growth of Crithidia at High Temperature: Crithidia hutneri sp. n. and Crithidia luciliae thermophila s. sp. n.* , 1977 .

[127]  Y. Eeckhout.  [Properties and location of the Trypanosomide "Crithidia luciliae" acid hydrolases]. , 1970, Archives Internationales de Physiologie et de Biochimie.

[128]  W. Gutteridge.  Some effects of pentamidine di-isethionate on Crithidia fasciculata. , 1969, The Journal of protozoology.

[129]  D. Wertlieb,et al.  Catalase in insect trypanosomatids. , 1963, The Journal of protozoology.

[130]  P. Schmid-Hempel,et al.  Few colonies of the host Bombus terrestris disproportionately affect the genetic diversity of its parasite, Crithidia bombi. , 2014, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[131]  J. Lukeš,et al.  Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed. , 2013, Trends in parasitology.

[132]  M. Barrett,et al.  Multiple roles of proline transport and metabolism in trypanosomatids. , 2012, Frontiers in bioscience.

[133]  H. Michael G. Lattorff,et al.  A Quantitative In Vitro Cultivation Technique to Determine Cell Number and Growth Rates in Strains of Crithidia bombi (Trypanosomatidae), a Parasite of Bumblebees , 2011, The Journal of eukaryotic microbiology.

[134]  D. Maslov,et al.  Discovery and Barcoding by Analysis of Spliced Leader RNA Gene Sequences of New Isolates of Trypanosomatidae from Heteroptera in Costa Rica and Ecuador , 2007, The Journal of eukaryotic microbiology.

[135]  T. Souto-Padrón,et al.  Fine structure and cytochemistry of peroxisomes (microbodies) in Leptomonas samueli , 2004, Cell and Tissue Research.

[136]  T. A. Hall,et al.  BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT , 1999 .