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Protistology Mitochondrial Genomes of Amoebozoa
Protistology 13 (4), 179–191 (2019) Protistology Mitochondrial genomes of Amoebozoa Natalya Bondarenko1, Alexey Smirnov1, Elena Nassonova1,2, Anna Glotova1,2 and Anna Maria Fiore-Donno3 1 Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia 2 Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 194064 Saint Petersburg, Russia 3 University of Cologne, Institute of Zoology, Terrestrial Ecology, 50674 Cologne, Germany | Submitted November 28, 2019 | Accepted December 10, 2019 | Summary In this mini-review, we summarize the current knowledge on mitochondrial genomes of Amoebozoa. Amoebozoa is a major, early-diverging lineage of eukaryotes, containing at least 2,400 species. At present, 32 mitochondrial genomes belonging to 18 amoebozoan species are publicly available. A dearth of information is particularly obvious for two major amoebozoan clades, Variosea and Tubulinea, with just one mitochondrial genome sequenced for each. The main focus of this review is to summarize features such as mitochondrial gene content, mitochondrial genome size variation, and presence or absence of RNA editing, showing if they are unique or shared among amoebozoan lineages. In addition, we underline the potential of mitochondrial genomes for multigene phylogenetic reconstruction in Amoebozoa, where the relationships among lineages are not fully resolved yet. With the increasing application of next-generation sequencing techniques and reliable protocols, we advocate mitochondrial -
Testate Amoebae from South Vietnam Waterbodies with the Description of New Species Difflugia Vietnamicasp
Acta Protozool. (2018) 57: 215–229 www.ejournals.eu/Acta-Protozoologica ACTA doi:10.4467/16890027AP.18.016.10092 PROTOZOOLOGICA LSID urn:lsid:zoobank.org:pub:AEE9D12D-06BD-4539-AD97-87343E7FDBA3 Testate Amoebae from South Vietnam Waterbodies with the Description of New Species Difflugia vietnamicasp. nov. Hoan Q. TRANa, Yuri A. MAZEIb, c a Vietnamese-Russian Tropical Center, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Ha Noi, Vietnam b Department of Hydrobiology, Lomonosov Moscow State University, Moscow, Russia c Department of Zoology and Ecology, Penza State University, Penza, Russia Abstract. Testate amoebae in Vietnam are still poorly investigated. We studied species composition of testate amoebae in 47 waterbodies of South Vietnam provinces including natural lakes, reservoirs, wetlands, rivers, and irrigation channels. A total of 109 species and subspe- cies belonging to 16 genera, 9 families were identified from 191 samples. Thirty-five species and subspecies were observed in Vietnam for the first time. New speciesDifflugia vietnamica sp. nov. is described. The most species-rich genera are Difflugia (46 taxa), Arcella (25) and Centropyxis (14). Centropyxis aculeata was the most common species (observed in 68.1% samples). Centropyxis aerophila sphagniсola, Arcella discoides, Difflugia schurmanni and Lesquereusia modesta were characterised by a frequency of occurrence >20%. Other spe- cies were rarer. The species accumulation curve based on the entire dataset of this work was unsaturated and well fitted by equation S = 19.46N0.33. Species richness per sample in natural lakes and wetlands were significantly higher than that of rivers (p < 0.001). The result of the Spearman rank test shows weak or statistically insignificant relationships between species richness and water temperature, pH, dissolved oxygen, and electrical conductivity. -
Differential Gene Expression Analysis and Cytological Evidence Reveal a Sexual Stage of an Amoeba with Multiparental Cellular and Nuclear Fusion
PLOS ONE RESEARCH ARTICLE Differential gene expression analysis and cytological evidence reveal a sexual stage of an amoeba with multiparental cellular and nuclear fusion ☯ ☯ Yonas I. TekleID *, Fang Wang , Alireza Heidari, Alanna Johnson Stewart Department of Biology, Spelman College, Atlanta, Georgia, United States of America a1111111111 ☯ These authors contributed equally to this work. a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess a genetic toolkit necessary OPEN ACCESS for sexual reproduction. However, the mechanism of sexual development in a majority of Citation: Tekle YI, Wang F, Heidari A, Stewart AJ microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in (2020) Differential gene expression analysis and studying sex in microbial eukaryotes is a lack of observational evidence, primarily due to its cytological evidence reveal a sexual stage of an cryptic nature. In this study, we used a tractable fusing amoeba, Cochliopodium, to investi- amoeba with multiparental cellular and nuclear fusion. PLoS ONE 15(11): e0235725. https://doi. gate sexual development using stage-specific Differential Gene Expression (DGE) and org/10.1371/journal.pone.0235725 cytological analyses. Both DGE and cytological results showed that most of the meiosis and Editor: Arthur J. Lustig, Tulane University Health sex-related genes are upregulated in Cochliopodium undergoing fusion in laboratory culture. Sciences Center, UNITED STATES Relative gene ontology (GO) category representations in unfused and fused cells revealed Received: June 19, 2020 a functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. -
A Revised Classification of Naked Lobose Amoebae (Amoebozoa
Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility. -
Protist Phylogeny and the High-Level Classification of Protozoa
Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane). -
Vita: OR Anderson
CURRICULUM VITA O. Roger Anderson [Updated May 2020] BIRTH DATE: August 4, 1937 OCCUPATION: Microbial Physiological Ecologist, Biologist, and Educator PROFESSIONAL RANK: Professor of Natural Sciences, Columbia University T. C., 1964-present Teachers College ; Department Chairman, 1974-1980, 1993-1996, 2000-2017 Senior Research Scientist (Adj.), Biology, 1967-present Lamont-Doherty Earth Observatory of Columbia University Faculty Member at Large, Columbia University Graduate School of Arts and Sciences. 1993-present DEGREES: Bachelor of Arts (Botany) Washington University, St. Louis 1959 Master of Arts (Biological Education) Washington University 1961 Doctorate (Biology and Education) Washington University 1964 PROFESSIONAL EXPERIENCE (TEACHING): 1963-64 Washington University, St. Louis 1964-67 Assistant Professor of Natural Sciences Columbia University, Teachers College 1968-70 Associate Professor of Natural Sciences Columbia University, Teachers College 1971- Professor of Natural Sciences Columbia University, Teachers College 1992-1993 College Research Coordinator, Teachers College. 1993-1996 Associate Director, Division of Instruction, T. C. OFFICES IN NATIONAL AND INTERNATIONAL ORGANIZATIONS: 1976 President, National Association for Res. Science Teaching (International) 1993-95 President, Columbia University Chapter Sigma Xi Honorary Scientific Society (National) 1995 President, International Society of Protistology (International) ---------------------------------------------------------------------------------------------------- -
A Practical Implementation of Large Transcriptomic Data Analysis to Resolve Cryptic Species Diversity Problems in Microbial Eukaryotes Yonas I
Tekle and Wood BMC Evolutionary Biology (2018) 18:170 https://doi.org/10.1186/s12862-018-1283-1 RESEARCHARTICLE Open Access A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes Yonas I. Tekle* and Fiona C. Wood Abstract Background: Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances. Result: Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91–4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. -
Diversity, Phylogeny and Phylogeography of Free-Living Amoebae
School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science Diversity, phylogeny and phylogeography of free-living amoebae Ph.D. Thesis RNDr. Tomáš Tyml Supervisor: Mgr. Martin Kostka, Ph.D. Department of Parasitology, Faculty of Science, University of South Bohemia in České Budějovice Specialist adviser: Prof. MVDr. Iva Dyková, Dr.Sc. Department of Botany and Zoology, Faculty of Science, Masaryk University České Budějovice 2016 This thesis should be cited as: Tyml, T. 2016. Diversity, phylogeny and phylogeography of free living amoebae. Ph.D. Thesis Series, No. 13. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 135 pp. Annotation This thesis consists of seven published papers on free-living amoebae (FLA), members of Amoebozoa, Excavata: Heterolobosea, and Cercozoa, and covers three main topics: (i) FLA as potential fish pathogens, (ii) diversity and phylogeography of FLA, and (iii) FLA as hosts of prokaryotic organisms. Diverse methodological approaches were used including culture-dependent techniques for isolation and identification of free-living amoebae, molecular phylogenetics, fluorescent in situ hybridization, and transmission electron microscopy. Declaration [in Czech] Prohlašuji, že svoji disertační práci jsem vypracoval samostatně pouze s použitím pramenů a literatury uvedených v seznamu citované literatury. Prohlašuji, že v souladu s § 47b zákona č. 111/1998 Sb. v platném znění souhlasím se zveřejněním své disertační práce, a to v úpravě vzniklé vypuštěním vyznačených částí archivovaných Přírodovědeckou fakultou elektronickou cestou ve veřejně přístupné části databáze STAG provozované Jihočeskou univerzitou v Českých Budějovicích na jejích internetových stránkách, a to se zachováním mého autorského práva k odevzdanému textu této kvalifikační práce. -
Protista (PDF)
1 = Astasiopsis distortum (Dujardin,1841) Bütschli,1885 South Scandinavian Marine Protoctista ? Dingensia Patterson & Zölffel,1992, in Patterson & Larsen (™ Heteromita angusta Dujardin,1841) Provisional Check-list compiled at the Tjärnö Marine Biological * Taxon incertae sedis. Very similar to Cryptaulax Skuja Laboratory by: Dinomonas Kent,1880 TJÄRNÖLAB. / Hans G. Hansson - 1991-07 - 1997-04-02 * Taxon incertae sedis. Species found in South Scandinavia, as well as from neighbouring areas, chiefly the British Isles, have been considered, as some of them may show to have a slightly more northern distribution, than what is known today. However, species with a typical Lusitanian distribution, with their northern Diphylleia Massart,1920 distribution limit around France or Southern British Isles, have as a rule been omitted here, albeit a few species with probable norhern limits around * Marine? Incertae sedis. the British Isles are listed here until distribution patterns are better known. The compiler would be very grateful for every correction of presumptive lapses and omittances an initiated reader could make. Diplocalium Grassé & Deflandre,1952 (™ Bicosoeca inopinatum ??,1???) * Marine? Incertae sedis. Denotations: (™) = Genotype @ = Associated to * = General note Diplomita Fromentel,1874 (™ Diplomita insignis Fromentel,1874) P.S. This list is a very unfinished manuscript. Chiefly flagellated organisms have yet been considered. This * Marine? Incertae sedis. provisional PDF-file is so far only published as an Intranet file within TMBL:s domain. Diplonema Griessmann,1913, non Berendt,1845 (Diptera), nec Greene,1857 (Coel.) = Isonema ??,1???, non Meek & Worthen,1865 (Mollusca), nec Maas,1909 (Coel.) PROTOCTISTA = Flagellamonas Skvortzow,19?? = Lackeymonas Skvortzow,19?? = Lowymonas Skvortzow,19?? = Milaneziamonas Skvortzow,19?? = Spira Skvortzow,19?? = Teixeiromonas Skvortzow,19?? = PROTISTA = Kolbeana Skvortzow,19?? * Genus incertae sedis. -
Marine Biological Laboratory) Data Are All from EST Analyses
TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878. -
THE THECAMOEBIAN BIBLIOGRAPHY 2Nd Edition
Palaeontologia Electronica http://palaeo-electronica.org Preamble to the 2nd Edition. Since the publication of the first edition we have collected about 1,000 new titles which are inserted in the second edition. All the remarks and caveats in the Introduction are valid for both editions. The first edition of this document was published in 1999. THE THECAMOEBIAN BIBLIOGRAPHY 2nd Edition F.S. Medioli, L. Bonnet, David B. Scott, and Barbara Elizabeth Medioli ABSTRACT The literature on thecamoebians can be rather confusing, partly because it has been published in many different languages, but mainly because these Rhizopoda have been the subject of study for a wide array of researchers with very different inter- ests. Not only has this resulted in fragmentation of the literature due to research results being published in journals specializing in different fields, but inevitably has also resulted in development of a chaotic terminology and nomenclature. For example there is even confusion as to what to call the group, as terms such as "rhizopods," "testate amoebae," and "arcellaceans" have all been used by various authors as synonyms of "Thecamoebians." Even more confusing is the nomenclature of the described the- camoebian species. Lack of access to the literature and limited interchange between the various research groups has generated many synonyms. Although only a first step this fairly complete bibliography on thecamoebians has been compiled to assist researchers become more aware of the available literature. F.S. Medioli, David B. Scott. Dalhousie University, Department of Earth Sciences, Halifax, Nova Scotia, B3H 3J5, Canada. [email protected]. [email protected]. -
Freshwater Silica-Scaled Heterotrophic Protista: Heliozoa, Thaumatomonad Flagellates, Amoebae, and Bicosoecids, from the Lake Itasca Region, Minnesota
JOURNAL OF THE MINNESOTA ACADEMY OF SCIENCE VOL. 78 NO. 2 (2015) FRESHWATER SILICA-SCALED HETEROTROPHIC PROTISTA: HELIOZOA, THAUMATOMONAD FLAGELLATES, AMOEBAE, AND BICOSOECIDS, FROM THE LAKE ITASCA REGION, MINNESOTA Daniel E. Wujek Central Michigan University, Mt. Pleasant, MI Forty-nine plankton samples were collected from the Lake Itasca Region, Minnesota over a period sporadically covering the summers of 1980, 1981 and 1987. A total of 22 freshwater heterotrophic siliceous-scaled species were observed: 18 heliozoa, two thaumatomonad flagellates, one bicosoecid, and one testate amoeba. Scale identifications were based on transmission electron microscopy. New records for North America include two heliozoans and one thaumatomonad flagellate. Five heliozoa taxa and one thaumatomonad flagellate are new records for the U.S. Wujek DE. Freshwater silica-scaled heterotrophic protista: heliozoa, thaumatomonad flagellates, amoebae, and bicosoecids, from the Lake Itasca Region, Minnesota. Minnesota Academy of Science Journal. 2015; 78(2):1-14. Keywords: bicosoecids, heliozoa, protista, testate amoeba, thaumatomonad flagellates Daniel E Wujek, Department of Biology, Central microscopy (EM) usually is necessary to distinguish Michigan University, Mt. Pleasant, MI 48859, e- sufficient morphology for species identification in the mail: [email protected]. scaled chrysophyte groups3 and now have become the This study was in part funded by a grant from the tool for other scaled protists. CMU FRCE committee. North American heterotrophic protist studies