DOCSLIB.ORG

Fungal Transposable Elements: Generators of Diversity and Genetic Tools

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Fungal Transposable Elements: Generators of Diversity and Genetic Tools J. Gener., Vol. 75, Number 3, December 1996, pp. 325-339. ((') Indian Academy of Sciences Fungal transposable elements: generators of diversity and genetic tools M. J. DABOUSSI Institut de G6n6tique et Microbiologie, Universit~ Paris-Sud, 91405 Orsay, France Abstract. Representatives of several classes of transposable elements (TEs) have been characterized in a broad range of fungal species. The studies indicate flint these elements are ancient and ubiquitous components of fungal genomes. Some of these elements have been shown to actively affect gene structure and function in several ways: inactivation of gene expression upon insertion, modification of the nucleotide sequence through excision, and probably by inducing extensive chromosomal rearrangements. The ability o['TEs to generate a high degree of genetic diversity may therefore be important in the evolution of the fungal genome. TEs also have many potential applications in genetic research, including inserfional mumgenesis and population fingerprinting, as well as gene transfer within and between species. All these genetic approaches are important as tools in studies &molecular biology and evolution of fungal species, many of which lack a functional sexual cycle. Keywords. Transposable elements; mutagenesis; filamentous fungi; genetic application. 1. Introduction Filamentous fungi have proved to be valuable in the development of many fundamen- tal ideas: these include the one gene-one enzyme concept (Neurospora crassa), models for recombination (Ascobolus immersus), and regulation of gene expression (Aspergillus nidulans). However, there is one area where fungi, particularly filamentous fungi, were long silent; that is the area of transposable elements (TEs). It is now more than four decades since Barbara McClintock developed the concept of transposable genetic elements through genetic studies in maize. Since then, such elements have been found in a wide range of organisms from bacteria to higher eukaryotes (see Berg and Howe 1989 for a review) and are presumed to be ubiquitous. However, with the notable exception of Ty elements in the yeast Saccharomyces cerevisiae (Boeke 1989), very little was known until a few years ago about the incidence and properties of TEs in other fungal species. This was probably due to the fact that the laboratory strains of the best-studied ascomycetes, A. nidulans and N. crassa, appear to be devoid of active transposons. In another ascomycete, A. immersus, genetic elements with properties of classical transposons associated wih genetic instabilities were reported but not characterized at the molecular level (Decaris et al. 1978). In the past few years our picture of fungal transposons has grown considerably as a result of work with species from different phylogenetic groups and ecological situations: plant pathogens, and industrial and field strains (see reviews by Oliver 1992 and Dobinson and Hamer 1993). Many different classes of TEs are now known in different species of ascomycetes (listed in this review), and TEs have recently been reported in phycomycetes (Avalos et al. 1996) and basidiornycetes (Gaskell et al. 1995), opening a door of opportunity for genetic research. The aim of this paper is to review progress made in the molecular-genetic analysis of these fungal transposons. Emphasis will be on what is known about their mechanisms of transposition and their consequences to 325 326 M. J. Daboussi the host genome, the spread of transposons within and between species, and finally the potential use of transposons for genetic research. 2. Structural features of fungal transposons Fungal transposons have been identified using a variety of strategies (figure 1) that exploit the two main characteristics of TEs: (i) they are present in multiple copies in the genome and thus can be discovered by analysing dispersed repetitive sequences, and (ii) they can move from one position to another in the genome, and therefore can be trapped through their insertion in a selected gene. Using the first strategy, different transposon- like sequences have been recognized by comparison with the known transposon sequences from other organisms, although we do not know if these transposon-like sequences are still active. The most satisfactory way to screen for active transposons is the transposon trapping approach, which is based on spontaneous inactivation of a cloned gene. This strategy is usually applied to genes whose mutant phenotypes can be positively screened. Examples of this approach are the am gene coding for glutamate dehyd- rogenase which allowed the discovery of the Tad element in N. crassa (Kinsey and Helber 1989), and mutations in the nia gene encoding nitrate reductase which can be selected through resistance to chlorate (Cove 1976). Trapping using the nia gene has been very efficient in Fusarium oxysporum (Daboussi and Langin 1994) and has been successfully applied to other fungal species, leading to identification of at least eight different mobile elements. Finally, some other elements have been found using heterologous hybridiz- ation or have been discovered fortuitously through DNA sequencing. The TEs or sets of related sequences identified in fungal genomes reflect the whole spectrum of eukaryotic transposable elements. Their general structural features are summarized in figure 1. Representatives of the two classes of transposable elements are found in fungi: those that transpose by reverse transcription of an RNA copy of the element (class I) and those that probably transpose directly through DNA copies (class II) (Finnegan 1989; McDonald 1993). Class I elements are LTR (long terminal repeats) retrotransposons that belong mostly to the gypsy group: Foret and skippy in F. oxysporum (Julien et al. 1992; Anaya and Roncero 1995), grh and MAGGYin Magnaporthe grisea (Dobinson et aI. 1993; Farman et aI. 1996a), CfT-1 in Cladosporium fulvum (McHale et al. 1989, 1992), Boty in Botrytis cinerea (Diolez et al. 1995), Afutl in Aspergillus fumigatus (Neuv6glise et al. 1996a) and Mars4 in Ascobolus immersus (Goyon et al. 1996). Only Mars2 of A. immersus is a copia-like element (Goyon et al. 1996). Several non-LTR retrotransposons with structural features of LINEs (long inter- spersed nuclear elements) have been characterized: Tad, an element of N. crassa, the first transposable element reported in fungi (Kinsey and Helber 1989), MGR583 in M. grisea (Hamer et. al. 1989), Palm in F. oxysporum (Mouyna et al. 1996), Mars1 in A. immersus (Goyon et al. 1996), and CgT-I in ColIetotrichum gloeosporioides (He et al. 1996). SINE (short interspersed nuclear element)-like elments have also been recog- nized: Nrsl in Nectria haematococca (Kim er aI. 1995), MGSR1 and Mg-SINE in M. grisea (Sone et al. 1993; Kachroo et aI. 1995), as well as Eg-RI and EGH in Erysiphe (Rasmussen et at. 1993; Wei et aI. 1996). Class II or DNA transposons of different types have also been isolated, most of them after transposition in the nia gene. Some of them are representatives of families Fungal transposable elements 327 Class h Retroelements LTR-RETROTRANSPOSON8 type Example 5' LTR ~Ta~ pOt ~ ? 3' LTR Feint t~) and skippy f3; iF. e~ysporumJ gypsy grh O) and MAGGYCt.;) (M. grisee) CtT-I r futvum); Boty ~r tin~ Afu110) (A. fumJg~tus); Mars4 (.4, immersus) 5' LTR gag pol 3' LTR copia Mars2 (~ (A. immersus) non LTFI-RETROTRANSPOSONS 5. gag? 3' Tad ~2)(N, erassa); PalmOJ iF. oxysporum) MGR583 (1)(M, grisea); Mars1 (~)(A. imrnersLts) CgT1 (IJ(C. gtoeospo[ioides) Nrs l O) (N. haematocc~eca) MGSRI {=)and Mg,BtNEII) (M. gfises) Eg-R1 ilt(E, graminis) and EGH (g(E. hordei) Class Ih DNA transposons Tc I/mariner impatel2) (F.oxysporumy Ant1 (~(A. niger) IR IR Fort {2~arid For2 (2~ (F.ox3,sporurn);Ta~ {2>(A.nigsO Pot2 (1~and MGR586 (~) (M. Grisea); Flipper {~J(B, cinerea); Puntr~ iN. crassa) A c-like Ascot ft) and Tasce I~) (A. imrnemus); restless (lilT. Inflaturn) Hop (a~ (F.oxysporctm) UnreLated Pc~ (P. chrysosporlum) Unclassified Guest (S)(N, cr~a) Figure. 1. Schematic representations of the structural features of fungal transposable ele- ments. For purposes of clarity, the overall size of the elements is not to scale. Arrows denote the short duplication (TSD) generated in the host genera~ during transposition. There are two types of class I elements. LTR-retrotransposons resemble retroviruses in having long terminal direct repeats (LTR) flanking an internal domain encoding proteins analogous to the gag and pol retroviral gone products. They are divided into two groups, the gypsy and the copia types, on the basis of the order of functional domains in the pot gone (PR, protease; RT, reverse transcriptase; RH, RNAase H; 1N, integrase) and the presence or not of a third ORF in a position similar to that of the viral env gone but with no structural or functional homology to it. The non-LTR-retrotransposons lack terminal repeats and carry a poly(A) taft at their 3' ends. They fall into two families similar to the long and short interspersed nuclear elements described in mammals and referred to as LINEs and SINEs respectively. LINE-like elements commonly possess two long ORFs, with similarities to ~]c~,]as well as RT and RH genes, and are often deleted in their 5' ends. SINE-like elements are short elements wl~ich contain an internal RNA polymerase Ill promoter with a bipartite structure represented by the A and B boxes and which rely on RT for mobilization but do not themselves encode the enzyme. Class II elements share the same basic design of short inverLed terminal repeats (IR) bordering one or more ORFs, encoding transposase, an enzyme required for their own transposition. Some very short elements with IR and potential to form a hairpin structure are difficult to classify at present. Numbers within brackets indicate the strategy used to identify the transposable element: (1) isolated by cloning band of repetitive DNA; (2) isolated after transposition within the nia gone, with the exception of Tad, which was transposed into the am gone, and Ascot, which preexisted as an insertion in the b2 gone; (3) isolated by differential screening with antibodies against RT; (4) isolated using a CfT-1 heterologous probe; (5) identified through gone sequcncing.
Load more

Recommended publications
  • Identification of a Non-LTR Retrotransposon from the Gypsy Moth
    Insect Molecular Biology (1999) 8(2), 231-242 Identification of a non-L TR retrotransposon from the gypsy moth K. J. Garner and J. M. Siavicek sposons (Boeke & Corces, 1989), or retroposons USDA Forest Service, Northeastern Research Station, (McClure, 1991). Many non-L TR retrotransposons Delaware, Ohio, U.S.A. have been described in insects, including the Doc (O'Hare et al., 1991), F (Di Nocera & Casari, 1987), I (Fawcett et al., 1986) and jockey (Priimiigi et al., 1988) Abstract elements of Drosophila melanogaster, the T1Ag A family of highly repetitive elements, named LDT1, (Besansky, 1990) and Q (Besansky et al., 1994) ele- has been identified in the gypsy moth, Lymantria ments of Anopheles gambiae, and the R1Bm (Xiong & dispar. The complete element is 5.4 kb in length and Eickbush, 1988a) and R2Bm (Burke et al., 1987) lacks long-terminal repeats, The element contains two families of ribosomal DNA insertions in Bombyx mori. open reading frames with a significant amino acid Gypsy moths (Lymantria dispar) are currently wide- sequence similarity to several non-L TR retrotrans- spread forest pests in the north-eastern United States posons. The first open reading frame contains a and the adjacent regions of Canada. Population region that potentially encodes a polypeptide similar markers have been sought to distinguish the North to DNA-binding GAG-like proteins. The second American gypsy moths introduced from Europe in 1869 encodes a polypeptide resembling both endonuclease from those recently introduced from Asia (Bogdano- and reverse transcriptase sequences. A" members of wicz et al., 1993; Pfeifer et al., 1995; Garner & Siavicek, the LDT1 element family sequenced thus far have poly- 1996; Schreiber et al., 1997).
    [Show full text]
  • The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease
    The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease by Sepehr Ehsani A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto © Copyright by Sepehr Ehsani 2012 The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease Sepehr Ehsani Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto 2012 Abstract The cellular prion protein (PrPC) is unique amongst mammalian proteins in that it not only has the capacity to aggregate (in the form of scrapie PrP; PrPSc) and cause neuronal degeneration, but can also act as an independent vector for the transmission of disease from one individual to another of the same or, in some instances, other species. Since the discovery of PrPC nearly thirty years ago, two salient questions have remained largely unanswered, namely, (i) what is the normal function of the cellular protein in the central nervous system, and (ii) what is/are the factor(s) involved in the misfolding of PrPC into PrPSc? To shed light on aspects of these questions, we undertook a discovery-based interactome investigation of PrPC in mouse neuroblastoma cells (Chapter 2), and among the candidate interactors, identified two members of the ZIP family of zinc transporters (ZIP6 and ZIP10) as possessing a PrP-like domain. Detailed analyses revealed that the LIV-1 subfamily of ZIP transporters (to which ZIPs 6 and 10 belong) are in fact the evolutionary ancestors of prions (Chapter 3).
    [Show full text]
  • Using Rnai to Elucidate Mechanisms of Human Disease
    Cell Death and Differentiation (2008) 15, 809–819 & 2008 Nature Publishing Group All rights reserved 1350-9047/08 $30.00 www.nature.com/cdd Review From sequence to function: using RNAi to elucidate mechanisms of human disease NM Wolters1 and JP MacKeigan*,1 RNA interference (RNAi) has emerged as one of the most powerful tools for functionally characterizing large sets of genomic data. Capabilities of RNAi place it at the forefront of high-throughput screens, which are able to span the human genome in search of novel targets. Although RNAi screens have been used to elucidate pathway components and discover potential drug targets in lower organisms, including Caenorhabditis elegans and Drosophila, only recently has the technology been advanced to a state in which large-scale screens can be performed in mammalian cells. In this review, we will evaluate the major advancements in the field of mammalian RNAi, specifically in terms of high-throughput assays. Crucial points of experimental design will be highlighted, as well as suggestions as to how to interpret and follow-up on potential cell death targets. Finally, we assess the prospective applications of high-throughput screens, the data they are capable of generating, and the potential for this technique to further our understanding of human disease. Cell Death and Differentiation (2008) 15, 809–819; doi:10.1038/sj.cdd.4402311; published online 18 January 2008 The sequencing of the human genome ushered a new era into maintaining the balance between cell survival, cell death, the field of modern biology; it is now possible to elucidate and autophagy represents a crucial regulatory point in human molecular pathways relevant to development and disease health and that when this balance is tipped, a variety of with a breadth never before seen.
    [Show full text]
  • The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads
    www.nature.com/scientificreports OPEN The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads Liliya Doronina1,*, Andreas Matzke1,*, Gennady Churakov1,2, Monika Stoll3, Andreas Huge3 & Jürgen Schmitz1 Received: 13 October 2016 Solving problematic phylogenetic relationships often requires high quality genome data. However, Accepted: 25 January 2017 for many organisms such data are still not available. Among rodents, the phylogenetic position of the Published: 03 March 2017 beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy- free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). Most of an organism’s phylogenetic history is fossilized in their heritable genomic material. Using data from genome sequencing projects, particularly informative regions of this material can be extracted in sufficient num- bers to resolve the deepest history of speciation.
    [Show full text]
  • A Field Guide to Eukaryotic Transposable Elements
    GE54CH23_Feschotte ARjats.cls September 12, 2020 7:34 Annual Review of Genetics A Field Guide to Eukaryotic Transposable Elements Jonathan N. Wells and Cédric Feschotte Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; email: [email protected], [email protected] Annu. Rev. Genet. 2020. 54:23.1–23.23 Keywords The Annual Review of Genetics is online at transposons, retrotransposons, transposition mechanisms, transposable genet.annualreviews.org element origins, genome evolution https://doi.org/10.1146/annurev-genet-040620- 022145 Abstract Annu. Rev. Genet. 2020.54. Downloaded from www.annualreviews.org Access provided by Cornell University on 09/26/20. For personal use only. Copyright © 2020 by Annual Reviews. Transposable elements (TEs) are mobile DNA sequences that propagate All rights reserved within genomes. Through diverse invasion strategies, TEs have come to oc- cupy a substantial fraction of nearly all eukaryotic genomes, and they rep- resent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic be- havior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species. 23.1 Review in Advance first posted on , September 21, 2020.
    [Show full text]
  • Mg-SINE: a Short Interspersed Nuclear Element from the Rice Blast Fungus, Magnaporthe Grisea (Transposon/Repeated DNA) PRADEEP KACHROO*, SALLY A
    Proc. Natl. Acad. Sci. USA Vol. 92, pp. 11125-11129, November 1995 Genetics Mg-SINE: A short interspersed nuclear element from the rice blast fungus, Magnaporthe grisea (transposon/repeated DNA) PRADEEP KACHROO*, SALLY A. LEONGt, AND BHARAT B. CHATTOO*t *Department of Microbiology and Biotechnology Center, Faculty of Science, M. S. University of Baroda, Baroda 390 002, India; and tU.S. Department of Agriculture-Agricultural Research Service Plant Disease Research Unit, 1630 Linden Drive, University of Wisconsin, Madison, WI 53706 Communicated by M. S. Swaminathan, M. S. Swaminathan Research Foundation, Madras, India, June 28, 1995 ABSTRACT A short interspersed nuclear element, Mg- Magnaporthe grisea, an ascomycetous fungus responsible for SINE, was isolated and characterized from the genome of the the blast disease of rice (Oryza sativa), is known to generate rice blast fungus, Magnaporthe grisea. Mg-SINE was isolated new pathogenic variants at a high frequency (15). Various as an insertion element within Pot2, an inverted-repeat trans- mechanisms have been postulated to explain pathogenic vari- poson from M. grisea and shows typical features of a mam- ability in this fungus (15-17), although its molecular basis malian SINE. Mg-SINE is present as a 0.47-kb interspersed remains elusive. We initiated an analysis of repeated DNA sequence at "100 copies per haploid genome in both rice and sequences of M. grisea in order to delineate their role in non-rice isolates of M. grisea, indicating a common evolution- genome organization and generation of variability. We report ary origin. Secondary structure analysis ofMg-SINE revealed here the presence of a SINE sequence in the genome of M.
    [Show full text]
  • 5' Exonuclease ERL1 in Chloroplast Ribosomal RNA
    Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) im Fachbereich 18 - Naturwissenschaften der Universität Kassel vorgelegt von: Heiko Tobias Schumacher Kassel im Mai 2009 Datum der Disputation: 16. Juli 2009 Die Natur ist aller Meister Meister, sie zeigt uns erst den Geist der Geister Johann Wolfgang v. Goethe Erklärung Hiermit versichere ich, dass ich die vorliegende Dissertation selbständig und ohne unerlaubte Hilfe angefertigt und andere als die in der Dissertation angegebenen Hilfsmittel nicht benutzt habe. Alle Stellen, die wörtlich oder sinngemäß aus veröffentlichten oder unveröffentlichten Schriften entnommen sind, habe ich als solche kenntlich gemacht. Kein Teil dieser Arbeit ist in einem anderen Promotions- oder Habilitationsverfahren verwendet worden. Kassel, den 03. Mai 2009 __________________________________ Heiko Tobias Schumacher Zusätzliche Erklärung über kooperative Arbeiten und Publikation Teile der in dieser Dissertation präsentierten Resultate sind das Ergebnis kooperativer Arbeiten von Heiko Tobias Schumacher (Universität Kassel) und Jutta Maria Helm (Universität für Bodenkultur Wien) am Institut für Molekularbiologie und Biotech- nologie in Heraklion, Griechenland. Die folgenden Arbeiten wurden von Jutta Maria Helm durchgeführt: • Herstellung transgener Nicotiana benthamiana-Pflanzen zur Überexpression bzw. Suppression von ERL1 (vergl. Abschnitt 2.2.6.). • Herstellung doppelt-homozygoter Kreuzungen zwischen der GFP-exprimieren- den Nicotiana benthamiana-Linie GFP 6.4 mit ERL1-überexprimierenden Pflan- zen (vergl. Abschnitt 3.3.2.). • Chlorophyll a Fluoreszenz-Messungen zur Charakterisierung grundlegender bioenergetischer Parameter in ERL1-überexprimierenden Pflanzen (vergl. Ab- schnitt 3.4.3.). • Klonierung kleiner ribosomaler RNAs zur Analyse der 3’-Enden pflanzlicher 5.8S, 5S und 4.5S rRNAs (vergl. Abschnitte 2.2.11. und 3.6.1.). Der Elektronenmikroskop-Service wurde von Eva Papadogiorgaki geleitet.
    [Show full text]
  • Sva Elements: Hominid Specific Retrotransposons
    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2006 SVA elements: hominid specific etrr otransposons Hui Wang Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Wang, Hui, "SVA elements: hominid specific er trotransposons" (2006). LSU Doctoral Dissertations. 2016. https://digitalcommons.lsu.edu/gradschool_dissertations/2016 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. SVA ELEMENTS: HOMINID SPECIFIC RETROTRANSPOSONS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences By Hui Wang B.S., Shanghai Jiao Tong University, P.R.China, 2000 M.S., Shanghai Jiao Tong University, P.R.China, 2003 December 2006 ACKNOWLEDGEMENTS I would like to thank Dr. Mark A. Batzer, my advisor, for his continuous guidance, constant encouragement, and financial support during my Ph.D study at LSU. It is my great pleasure to learn from and work with such a knowledgeable, considerate, and helpful scholar. I want to express my sincere gratitude to my committee members, Dr. David Donze, Dr. Joomyeong Kim, Dr. Stephania Cormier and Dr. Karin Peterson. I would like to thank all of them for kindly serving on my committee. Also I want to thank members in the Batzer’s laboratory for their scientific guidance and friendship, especially to Dr.
    [Show full text]
  • Retroposon Analysis and Recent Geological Data Suggest Near-Simultaneous Divergence of the Three Superorders of Mammals
    Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals Hidenori Nishiharaa, Shigenori Maruyamab, and Norihiro Okadaa,1 aDepartment of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-21 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; and bDepartment of Earth and Planetary Sciences, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan Edited by Masatoshi Nei, Pennsylvania State University, University Park, PA, and approved February 13, 2009 (received for review September 17, 2008) As a consequence of recent developments in molecular phylog- (9). They estimated molecular divergence times among many enomics, all extant orders of placental mammals have been mammalian orders to be Ϸ100 Ma, which is inconsistent with grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, fossil records suggesting that most mammals had diverged after which originated in Africa, South America, and Laurasia, respec- 65 Ma. One of their interpretations was that the early divergence tively. Despite this advancement, the order of divergence of these of mammals occurred because of several continental fissions. 3 lineages remains unresolved. Here, we performed extensive This hypothesis prompted many biologists to consider available retroposon analysis with mammalian genomic data. Surprisingly, geological data when estimating lineage divergence. One of the we identified a similar number of informative retroposon loci that outcomes of this idea is Afrotheria, which is a good represen- support each of 3 possible phylogenetic hypotheses: the basal tative case for the association between continental drift and position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreoth- mammalian evolution (10, 11).
    [Show full text]
  • Downloads/Repeatmaskedgenomes
    Kojima Mobile DNA (2018) 9:2 DOI 10.1186/s13100-017-0107-y REVIEW Open Access Human transposable elements in Repbase: genomic footprints from fish to humans Kenji K. Kojima1,2 Abstract Repbase is a comprehensive database of eukaryotic transposable elements (TEs) and repeat sequences, containing over 1300 human repeat sequences. Recent analyses of these repeat sequences have accumulated evidences for their contribution to human evolution through becoming functional elements, such as protein-coding regions or binding sites of transcriptional regulators. However, resolving the origins of repeat sequences is a challenge, due to their age, divergence, and degradation. Ancient repeats have been continuously classified as TEs by finding similar TEs from other organisms. Here, the most comprehensive picture of human repeat sequences is presented. The human genome contains traces of 10 clades (L1, CR1, L2, Crack, RTE, RTEX, R4, Vingi, Tx1 and Penelope) of non-long terminal repeat (non-LTR) retrotransposons (long interspersed elements, LINEs), 3 types (SINE1/7SL, SINE2/tRNA, and SINE3/5S) of short interspersed elements (SINEs), 1 composite retrotransposon (SVA) family, 5 classes (ERV1, ERV2, ERV3, Gypsy and DIRS) of LTR retrotransposons, and 12 superfamilies (Crypton, Ginger1, Harbinger, hAT, Helitron, Kolobok, Mariner, Merlin, MuDR, P, piggyBac and Transib) of DNA transposons. These TE footprints demonstrate an evolutionary continuum of the human genome. Keywords: Human repeat, Transposable elements, Repbase, Non-LTR retrotransposons, LTR retrotransposons, DNA transposons, SINE, Crypton, MER, UCON Background contrast, MER4 was revealed to be comprised of LTRs of Repbase and conserved noncoding elements endogenous retroviruses (ERVs) [1]. Right now, Repbase Repbase is now one of the most comprehensive data- keeps MER1 to MER136, some of which are further bases of eukaryotic transposable elements and repeats divided into several subfamilies.
    [Show full text]
  • 1 an ABBA-BABA Test for Introgression Using Retroposon
    bioRxiv preprint doi: https://doi.org/10.1101/709477; this version posted July 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. An ABBA-BABA Test for Introgression Using Retroposon Insertion Data Mark S. Springer and John Gatesy From the Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521 (Springer); Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 (Gatesy). Address correspondence to Mark S. Springer or J. Gatesy at the above addresses, or e- mail: [email protected] (Springer); [email protected] (Gatesy). Abstract DNA sequence alignments provide the majority of data for inferring phylogenetic relationships with both concatenation and coalescence methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroposon insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroposon insertions satisfy the 'no intralocus recombination' assumption of summary coalescence methods because they are singular events and better approximate neutrality relative to DNA sequences commonly applied in phylogenomic work. Retroposons have traditionally been analyzed with phylogenetic methods that ignore incomplete lineage sorting (ILS). Here, we analyze three retroposon data sets for mammals (Placentalia, Laurasiatheria, Balaenopteroidea) with two different ILS-aware methods. The first approach constructs a species tree from retroposon bipartitions with ASTRAL, and the second is a modification of SVD-Quartets. We also develop a χ2 Quartet-Asymmetry Test to detect hybridization using retroposon data.
    [Show full text]
  • Transposable Elements in Cancer and Other Human Diseases Benoît Chénais
    Transposable Elements in Cancer and Other Human Diseases Benoît Chénais To cite this version: Benoît Chénais. Transposable Elements in Cancer and Other Human Diseases. Cur- rent Cancer Drug Targets, Bentham Science Publishers, 2015, 15 (3), pp.227 - 242. 10.2174/1568009615666150317122506. hal-01905441 HAL Id: hal-01905441 https://hal.archives-ouvertes.fr/hal-01905441 Submitted on 25 Oct 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Mini review: Transposable Elements in Cancer and other Human Diseases Benoît Chénais* Mer Molécules Santé EA2160, UFR Sciences et Techniques, Université du Maine, Le Mans, France. *Corresponding Author: Chénais B., Mer Molécules Santé, UFR Sciences et Techniques, Université du Maine, Avenue Olivier Messiaen, F-72085 Le Mans Cedex, France, Tel:+33- 243-833-25; fax +33-243-833-917; Email: [email protected] Abstract: Transposable elements (TEs) are mobile DNA sequences representing a substantial fraction of most genomes. Through the creation of new genes and functions, TEs are important elements of genome plasticity and evolution. However TE insertion in human genomes may be the cause of genetic dysfunction and alteration of gene expression contributing to cancer and other human diseases.
    [Show full text]