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Supplementary figure 1. Maximum likelihood phylogenetic tree of the complete ScrollSaw dataset. The tree was inferred using IQ-TREE with LG+I+G4 model (the model selected by the program itself) with the ultrafast bootstrap algorithm and the SH-aLRT test (both 10000 replicates), as described under Materials and Methods. Dots at branches represent bootstrap values as indicated in the graphical legend (top right). Goniomonas avonlea Sar1b Tree scale: 0.1 SH-aLRT/UFboot Gloeochaete wittrockiana Sar1b >80/>95 Planomonas micra Sar1b >99/>99 Physarum polycephalum Sar1X Sar1L Bigelowiella natans SarL Raineriophrys erinaceoides Sar1b Gefionella okellyi Sar1b Goniomonas avonlea Sar1a Guillardia theta Sar1 Palpitomonas bilix Sar1 Cryptosporidium parvum Sar1 Symbiodinium minutum Sar1a Aplanochytrium kerguelense Sar1 Hyaloperonospora arabidopsidis Sar1 Nannochloropsis gaditana Sar1 Emiliania huxleyi Sar1a Pavlova sp. Sar1 Cyanophora paradoxa Sar1 Gloeochaete wittrockiana Sar1a1 Gloeochaete wittrockiana Sar1a2 Paratrimastix pyriformis Sar1 Chlamydomonas reinhardtii Sar1 Arabidopsis thaliana SarA1b Klebsormidium nitens Sar1 Planomonas micra Sar1a Capsaspora owczarzaki Sar1 Creolimax fragrantissima Sar1 Sar1 Sphaeroforma arctica Sar1 Acanthamoeba castellanii Sar1a Physarum polycephalum Sar1 Pygsuia biforma Sar1 Euglena gracilis Sar1 Thecamonas trahens Sar1 Gefionella okellyi Sar1a Andalucia godoyi Sar1 Adineta vaga Sar1a Drosophila melanogaster Sar1 Catenaria anguillulae Sar1 Aspergillus fumigatus Sar1 Coemansia reversa Sar1 Cryptococcus neoformans Sar1 Ustilago maydis Sar1 Spizellomyces punctatus Sar1 Basidiobolus meristosporus Sar1a Gonapodya prolifera Sar1 Monocercomonoides exilis Arl6 Paratrimastix pyriformis Arl6 Plasmodiophora brassicae Arl6 Amastigomonas sp. Arl6a Thecamonas trahens Arl6 Pygsuia biforma Arl6 Planomonas micra Arl6a Amastigomonas sp. Arl6b Andalucia godoyi Arl6 Gefionella okellyi Arl6 Malawimonas californiana Arl6 Emiliania huxleyi Arl6 Pavlova sp. Arl6 Palpitomonas bilix Arl6 Arl6 Phytophthora sojae Arl6 Vischeria sp. Arl6 Physarum polycephalum Arl6 Goniomonas avonlea Arl6 Guillardia theta Arl6 Cyanophora paradoxa Arl6 Gloeochaete wittrockiana Arl6 Batrachochytrium dendrobatidis Arl6 Spizellomyces punctatus Arl6 Mnemiopsis leidyi Arl6 Strongylocentrotus purpuratus Arl6 Nematostella vectensis Arl6 Trichoplax adhaerens Arl6 Gefionella okellyi Arfrp1 Malawimonas californiana Arfrp1 Goniomonas avonlea Arfrp1 Pygsuia biforma Arfrp1 Dictyostelium discoideum Arfrp1 Physarum polycephalum Arfrp1 Cyanophora paradoxa Arfrp1 Gloeochaete wittrockiana Arfrp1 Aurantiochytrium limacinum Arfrp1 Phytophthora sojae Arfrp1 Volvox carteri Arfrp1 Emiliania huxleyi Arfrp1 Pavlova sp. Arfrp1 Acanthamoeba castellanii Arfrp1 Euglena gracilis Arfrp1 Guillardia theta Arfrp1 Neovahlkampfia damariscottae Arfrp1 Arfrp1 Amastigomonas sp. Arfrp1 Thecamonas trahens Arfrp1 Palpitomonas bilix Arfrp1 Planomonas micra Arfrp1 Basidiobolus meristosporus Arfrp1 Phycomyces blakesleeanus Arfrp1 Batrachochytrium dendrobatidis Arfrp1 Spizellomyces punctatus Arfrp1 Trichoplax adhaerens Arfrp1 Nematostella vectensis Arfrp1 Strongylocentrotus purpuratus Arfrp1 Saccoglossus kowalevskii Arfrp1 Helobdella robusta Arfrp1 Ciona intestinalis Arfrp1 Homo sapiens Arfrp1 Paratrimastix pyriformis Arl13 Thecamonas trahens Arl13 Euglena gracilis Arl13 Euglena gracilis Arl13L3 Guillardia theta Arl13 Malawimonas californiana Arl13 Chlamydomonas reinhardtii Arl13 Volvox carteri Arl13 Physarum polycephalum Arl13 Naegleria gruberi Arl13 Goniomonas avonlea Arl13 Gefionella okellyi Arl13 Pygsuia biforma Arl13 Andalucia godoyi Arl13 Gloeochaete wittrockiana Arl13 Arl13 Planomonas micra Arl13 Cyanophora paradoxa Arl13 Homo sapiens Arl13b Takifugu rubripes Arl13b Ciona intestinalis Arl13 Capitella teleta Arl13 Saccoglossus kowalevskii Arl13 Palpitomonas bilix Arl13 Monocercomonoides exilis Arl13 Plasmodiophora brassicae Arl13 Pavlova sp. Arl13 Trichoplax adhaerens Arl13 Vischeria sp. Arl13 Euglena gracilis Arl16 Naegleria gruberi Arl16 Phytophthora sojae Arl16 Pavlova sp. Arl16 Micromonas commoda Arl16 Mastigamoeba balamuthi Arl16 Vischeria sp. Arl16 Andalucia godoyi Arl16 Gloeochaete wittrockiana Arl16 Cyanophora paradoxa Arl16 Arl16 Pygsuia biforma Arl16 Goniomonas avonlea Arl16 Physarum polycephalum Arl16 Gefionella okellyi Arl16 Malawimonas californiana Arl16 Paratrimastix pyriformis Arl16 Nematostella vectensis Arl16 Saccoglossus kowalevskii Arl16 Takifugu rubripes Arl16 Raineriophrys erinaceoides Arl18 Palpitomonas bilix Arl18 Paratrimastix pyriformis Arl18 Gefionella okellyi Arl18 Malawimonas californiana Arl18 Bodo saltans Arl18 Arl18 Perkinsela sp. Arl18 Planomonas micra Arl18 Ectocarpus siliculosus Arl18 Hyaloperonospora arabidopsidis Arl18 Spironucleus vortens Arl8 Paratrimastix pyriformis Arl8 Paramecium tetraurelia Arl8b Tetrahymena thermophila Arl8 Andalucia godoyi Arl8 Palpitomonas bilix Arl8 Gloeochaete wittrockiana Arl8 Reticulomyxa filosa Arl8b Cyanophora paradoxa Arl8 Goniomonas avonlea Arl8 Pavlova sp. Arl8 Raineriophrys erinaceoides Arl8a Coccomyxa subellipsoidea Arl8 Klebsormidium nitens Arl8 Physcomitrella patens Arl8b Neovahlkampfia damariscottae Arl8 Euglena gracilis Arl8 Arl8 Naegleria gruberi Arl8 Amastigomonas sp. Arl8 Thecamonas trahens Arl8 Planomonas micra Arl8 Acanthamoeba castellanii Arl8 Physarum polycephalum Arl8 Gefionella okellyi Arl8 Malawimonas californiana Arl8 Pygsuia biforma Arl8 Sphaeroforma arctica Arl8 Capsaspora owczarzaki Arl8 Homo sapiens Arl8a Batrachochytrium dendrobatidis Arl8 Basidiobolus meristosporus Arl8b Conidiobolus coronatus Arl8 Coemansia reversa Arl8 Physarum polycephalum Arl3 Gefionella okellyi Arl3a Malawimonas californiana Arl3 Pygsuia biforma Arl3 Planomonas micra Arl3 Andalucia godoyi Arl3 Goniomonas avonlea Arl3 Guillardia theta Arl3 Ectocarpus siliculosus Arl3 Vischeria sp. Arl3 Phytophthora sojae Arl3 Cyanophora paradoxa Arl3b Gloeochaete wittrockiana Arl3 Arl3 Paratrimastix pyriformis Arl3 Trichomonas vaginalis Arl3b Amastigomonas sp. Arl3 Thecamonas trahens Arl3 Pavlova sp. Arl3 Emiliania huxleyi Arl3a Emiliania huxleyi Arl3b Spizellomyces punctatus Arl3 Branchiostoma floridae Arl3 Takifugu rubripes Arl3a Capitella teleta Arl3 Saccoglossus kowalevskii Arl3 Andalucia godoyi Arl2 Ectocarpus siliculosus Arl2 Vischeria sp. Arl2 Symbiodinium minutum Arl2 Basidiobolus meristosporus Arl2 Phycomyces blakesleeanus Arl2 Catenaria anguillulae Arl2a Batrachochytrium dendrobatidis Arl2 Spizellomyces punctatus Arl2 Lottia gigantea Arl2 Capitella teleta Arl2 Saccoglossus kowalevskii Arl2 Takifugu rubripes Arl2 Hydra magnipapillata Arl2 Trichoplax adhaerens Arl2 Planomonas micra Arl2 Cyanophora paradoxa Arl2 Arl2 Gloeochaete wittrockiana Arl2 Aurantiochytrium limacinum Arl2 Amastigomonas sp. Arl2 Thecamonas trahens Arl2 Malawimonas californiana Arl2 Paratrimastix pyriformis Arl2 Emiliania huxleyi Arl2 Pavlova sp. Arl2 Goniomonas avonlea Arl2 Guillardia theta Arl2 Dictyostelium discoideum Arl2 Physarum polycephalum Arl2 Acanthamoeba castellanii Arl2 Amoebidium parasiticum Arl2 Pygsuia biforma Arl2 Giardia intestinalis Arf1 Spironucleus salmonicida Arf1 Arf1 Pygsuia biforma Arf6 Amoebidium parasiticum Arf6 Basidiobolus meristosporus Arf6a Andalucia godoyi Arf6 Arf6 Mastigamoeba balamuthi Arf6 Gefionella okellyi Arf6 Nannochloropsis gaditana Arf1 Ectocarpus siliculosus Arf1 Phytophthora sojae Arf1a Aurantiochytrium limacinum Arf1a Fonticula alba Arf1 Reticulomyxa filosa Arf1a Gefionella okellyi Arf1a Malawimonas californiana Arf1a Andalucia godoyi Arf1a Raineriophrys erinaceoides Arf1b Pygsuia biforma Arf1b Mastigamoeba balamuthi Arf1 Physarum polycephalum Arf1a Pygsuia biforma Arf1a Perkinsus marinus Arf1b Perkinsus marinus Arf1c Emiliania huxleyi Arf1a Pavlova sp. Arf1 Arf1 Amastigomonas sp. Arf1a Planomonas micra Arf1a Palpitomonas bilix Arf1 Basidiobolus meristosporus Arf1b Schizosaccharomyces pombe Arf1 Gonapodya prolifera Arf1a Spizellomyces punctatus Arf1 Spizellomyces punctatus Arf1b Gloeochaete wittrockiana Arf1 Selaginella moellendorffii ArfA1b Goniomonas avonlea Arf1a Amphimedon queenslandica Arf1a Nematostella vectensis Arf1b Coccomyxa subellipsoidea ArfA Klebsormidium nitens ArfA1 Oryza sativa ArfA1 Oryza sativa ArfA3a Neovahlkampfia damariscottae Arl5 Physarum polycephalum Arl5 Amastigomonas sp. Arl5 Thecamonas trahens Arl5 Spizellomyces punctatus Arl5 Basidiobolus meristosporus Arl5 Phycomyces blakesleeanus Arl5 Pygsuia biforma Arl5 Capsaspora owczarzaki Arl5 Adineta vaga Arl5b1 Drosophila melanogaster Arl5 Helobdella robusta Arl5 Goniomonas avonlea Arl5 Naegleria gruberi Arl5 Arl5 Raineriophrys erinaceoides Arl5 Klebsormidium nitens Arl5 Selaginella moellendorffii Arl5 Gloeochaete wittrockiana Arl5 Planomonas micra Arl5 Aurantiochytrium limacinum Arl5 Pavlova sp. Arl5 Palpitomonas bilix Arl5 Acanthamoeba castellanii Arl5 Malawimonas californiana Arl5 Gefionella okellyi Arl5 Euglena gracilis Arl5 Euglena gracilis Arl1 Neovahlkampfia damariscottae Arl1 Naegleria gruberi Arl1 Mastigamoeba balamuthi Arl1 Pygsuia biforma Arl1 Batrachochytrium dendrobatidis Arl1 Phycomyces blakesleeanus Arl1 Basidiobolus meristosporus Arl1b Catenaria anguillulae Arl1 Adineta vaga Arl1a Amoebidium parasiticum Arl1 Branchiostoma floridae Arl1 Sphaeroforma arctica rArl1 Guillardia theta Arl1 Cyanophora paradoxa Arl1 Gloeochaete wittrockiana Arl1 Emiliania huxleyi Arl1 Pavlova sp. Arl1 Arl1 Goniomonas avonlea Arl1 Aplanochytrium kerguelense Arl1 Vischeria sp. Arl1 Ostreococcus lucimarinus Arl1 Coccomyxa subellipsoidea Arl1 Volvox carteri Arl1 Acanthamoeba castellanii
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  • A Free-Living Protist That Lacks Canonical Eukaryotic DNA Replication and Segregation Systems

    A Free-Living Protist That Lacks Canonical Eukaryotic DNA Replication and Segregation Systems

    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.14.435266; this version posted March 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems 2 Dayana E. Salas-Leiva1, Eelco C. Tromer2,3, Bruce A. Curtis1, Jon Jerlström-Hultqvist1, Martin 3 Kolisko4, Zhenzhen Yi5, Joan S. Salas-Leiva6, Lucie Gallot-Lavallée1, Geert J. P. L. Kops3, John M. 4 Archibald1, Alastair G. B. Simpson7 and Andrew J. Roger1* 5 1Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Department of 6 Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2 2 7 Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom 8 3Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) 9 and University Medical Centre Utrecht, Utrecht, The Netherlands 10 4Institute of Parasitology Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic 11 5Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, 12 South China Normal University, Guangzhou 510631, China 13 6CONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y 14 energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih., México 15 7Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Department of 16 Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2 17 *corresponding author: [email protected] 18 D.E.S-L ORCID iD: 0000-0003-2356-3351 19 E.C.T.
  • Leishmania LABCG1 and LABCG2 Transporters

    Leishmania LABCG1 and LABCG2 Transporters

    Manzano et al. Parasites & Vectors (2017) 10:267 DOI 10.1186/s13071-017-2198-1 RESEARCH Open Access Leishmania LABCG1 and LABCG2 transporters are involved in virulence and oxidative stress: functional linkage with autophagy José Ignacio Manzano1, Ana Perea1, David León-Guerrero1, Jenny Campos-Salinas1, Lucia Piacenza2, Santiago Castanys1*† and Francisco Gamarro1*† Abstract Background: The G subfamily of ABC (ATP-binding cassette) transporters of Leishmania include 6 genes (ABCG1-G6), some with relevant biological functions associated with drug resistance and phospholipid transport. Several studies have shown that Leishmania LABCG2 transporter plays a role in the exposure of phosphatidylserine (PS), in virulence and in resistance to antimonials. However, the involvement of this transporter in other key biological processes has not been studied. Methods: To better understand the biological function of LABCG2 and its nearly identical tandem-repeated transporter LABCG1, we have generated Leishmania major null mutant parasites for both genes (ΔLABCG1-2). NBD-PS uptake, infectivity, metacyclogenesis, autophagy and thiols were measured. Results: Leishmania major ΔLABCG1-2 parasites present a reduction in NBD-PS uptake, infectivity and virulence. In addition, we have shown that ΔLABCG1-2 parasites in stationary phase growth underwent less metacyclogenesis and presented differences in the plasma membrane’s lipophosphoglycan composition. Considering that autophagy is an important process in terms of parasite virulence and cell differentiation, we have shown an autophagy defect in ΔLABCG1-2 parasites, detected by monitoring expression of the autophagosome marker RFP-ATG8. This defect correlates with increased levels of reactive oxygen species and higher non-protein thiol content in ΔLABCG1-2 parasites. HPLC analysis revealed that trypanothione and glutathione were the main molecules accumulated in these ΔLABCG1-2 parasites.
  • The Polar Lipidome of Cultured Emiliania Huxleyi: a Source of Bioactive Lipids with Relevance for Biotechnological Applications

    The Polar Lipidome of Cultured Emiliania Huxleyi: a Source of Bioactive Lipids with Relevance for Biotechnological Applications

    biomolecules Article The Polar Lipidome of Cultured Emiliania huxleyi: A Source of Bioactive Lipids with Relevance for Biotechnological Applications Susana S. Aveiro 1 ,Tânia Melo 2, Ana Figueiredo 1, Pedro Domingues 1 , Hugo Pereira 3, Inês B. Maia 4 , Joana Silva 5, M. Rosário Domingues 1,2 , Cláudia Nunes 6 and Ana S. P.Moreira 1,6,* 1 Mass Spectrometry Center, LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; [email protected] (S.S.A.); [email protected] (A.F.); [email protected] (P.D.); [email protected] (M.R.D.) 2 ECOMARE, CESAM—Centre for Environmental and Marine Studies, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; [email protected] 3 Green Colab—Associação Oceano Verde, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; [email protected] 4 Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; [email protected] 5 Allmicroalgae Natural Products S.A., Apartado 9, 2449-909 Pataias, Portugal; [email protected] 6 CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; [email protected] * Correspondence: [email protected]; Tel.: +351-234-401-505 Received: 14 September 2020; Accepted: 5 October 2020; Published: 12 October 2020 Abstract: Polar lipids from microalgae have aroused greater interest as a natural source of omega-3 (n-3) polyunsaturated fatty acids (PUFA), an alternative to fish, but also as bioactive compounds with multiple applications.
  • Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships Among Eukaryotic ‘‘Supergroups’’

    Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships Among Eukaryotic ‘‘Supergroups’’

    Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ‘‘supergroups’’ Vladimir Hampla,b,c, Laura Huga, Jessica W. Leigha, Joel B. Dacksd,e, B. Franz Langf, Alastair G. B. Simpsonb, and Andrew J. Rogera,1 aDepartment of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5; bDepartment of Biology, Dalhousie University, Halifax, NS, Canada B3H 4J1; cDepartment of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; dDepartment of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; eDepartment of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7; and fDepartement de Biochimie, Universite´de Montre´al, Montre´al, QC, Canada H3T 1J4 Edited by Jeffrey D. Palmer, Indiana University, Bloomington, IN, and approved January 22, 2009 (received for review August 12, 2008) Nearly all of eukaryotic diversity has been classified into 6 strong support for an incorrect phylogeny (16, 19, 24). Some recent suprakingdom-level groups (supergroups) based on molecular and analyses employ objective data filtering approaches that isolate and morphological/cell-biological evidence; these are Opisthokonta, remove the sites or taxa that contribute most to these systematic Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Exca- errors (19, 24). vata. However, molecular phylogeny has not provided clear evi- The prevailing model of eukaryotic phylogeny posits 6 major dence that either Chromalveolata or Excavata is monophyletic, nor supergroups (25–28): Opisthokonta, Amoebozoa, Archaeplastida, has it resolved the relationships among the supergroups. To Rhizaria, Chromalveolata, and Excavata. With some caveats, solid establish the affinities of Excavata, which contains parasites of molecular phylogenetic evidence supports the monophyly of each of global importance and organisms regarded previously as primitive Rhizaria, Archaeplastida, Opisthokonta, and Amoebozoa (16, 18, eukaryotes, we conducted a phylogenomic analysis of a dataset of 29–34).