DOCSLIB.ORG

The Hat-Family Transposable Element, Hopper, from Bactrocera Dorsalis Is a Functional Vector for Insect Germline Transformation Alfred M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Hat-Family Transposable Element, Hopper, from Bactrocera Dorsalis Is a Functional Vector for Insect Germline Transformation Alfred M Handler and Schetelig BMC Genetics 2020, 21(Suppl 2):137 https://doi.org/10.1186/s12863-020-00942-3 RESEARCH Open Access The hAT-family transposable element, hopper, from Bactrocera dorsalis is a functional vector for insect germline transformation Alfred M. Handler1* and Marc F. Schetelig2 Abstract Background: The hopper hAT-family transposable element isolated from the Oriental fruit fly, Bactrocera dorsalis,is distantly related to both the Drosophila hobo element and the Activator element from maize. The original 3120 bp hopperBd-Kah element isolated from the Kahuku wild-type strain was highly degenerate and appeared to have a mutated transposase and terminal sequences, while a second 3131 bp element, hopperBd-we, isolated from a white eye mutant strain had an intact transposase reading frame and terminal sequences consistent with function. Results: The hopperBd-we element was tested for function by its ability to mediate germline transformation in two dipteran species other than B. dorsalis. This was achieved by creating a binary vector/helper transformation system by linking the hopperBd-we transposase reading frame to a D. melanogaster hsp70 promoter for a heat-inducible transposase helper plasmid, and creating vectors marked with the D. melanogaster mini-white+ or polyubiquitin- regulated DsRed fluorescent protein markers. Conclusions: Both vectors were successfully used to transform D. melanogaster, and the DsRed vector was also used to transform the Caribbean fruit fly, Anastrepha suspensa, indicating a wide range of hopper function in dipteran species and, potentially, non-dipteran species. This vector provides a new tool for insect genetic modification for both functional genomic analysis and the control of insect populations. Keywords: Insect genetic modification, Transposon-mediated transformation, Tephritidae Background integration of DNA constructs greater than several kilo- Transposon-mediated germline transformation has been bases [2]. This limitation is especially critical for the de- the primary method of insect genomic manipulation velopment of genetically modified strains to improve since a P element vector was successfully transposed biologically-based strategies for the control of insect into the Drosophila melanogaster genome [1]. More re- populations harmful to agriculture and human health, cent gene-editing techniques, such as CRISPR/Cas9, for which conditional lethal and other transgene con- have provided additional methods for genome manipula- structs are typically 10 kb or greater. Significantly, gene- tion, but thus far are limited in achieving genomic editing is also limited in generating random genomic in- sertions for mutagenesis and enhancer-trap screens that have proven highly advantageous for functional genomic * Correspondence: [email protected] analysis, most clearly demonstrated by elucidating gene 1USDA/ARS, Center for Medical, Agricultural and Veterinary Entomology, 1700 SW 23rd Drive, Gainesville, FL 32608, USA function and regulation in the D. melanogaster model Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This is an open access article distributed under the terms of the Creative Commons Attribution IGO License (https://creativecommons.org/licenses/by/3.0/igo/) which permits unrestricted use, distribution, and reproduction in any medium, provided appropriate credit to the original author(s) and the source is given. Handler and Schetelig BMC Genetics 2020, 21(Suppl 2):137 Page 2 of 9 system. Thus, the ability to use transposon vector sys- site sequence consistent with a functional transposon. tems such as the P element in a wide range of insect sys- While this full-length element provided insights into the tems has been, and remains, a high priority for conserved functional domains for Class II elements in understanding and manipulating insect genomes. general, and hAT elements specifically, its ability to au- Unfortunately, P element mobility was found to be tonomously transpose (requiring functional transposase atypically limited to the Drosophila genus and closely re- and requisite terminal sequences) remained unknown. lated species and has never been successfully used to Function for hopperBd-we was implied by preliminary em- achieve transposon-mediated transformation in a non- bryonic transposon mobility assays in B. dorsalis, how- drosophilid species [3]. More than a decade passed be- ever, function for the D. melanogaster hobo hAT fore other Class II transposable elements were discov- element was also implied for five tephritid species using ered that were functionally less restricted and successful simlar assays [16], yet in our hands it was never success- in achieving non-drosophilid transformation, which in- ful in achieving non-drosophilid germline transform- cluded mariner/Mos1 discovered in D. mauritiana that ation. Thus, we initiated more direct and conclusive initially transformed Aedes aegypti [4, 5], Minos discov- tests for hopperBd-we function based on its ability to me- ered in D. hydei that initially transformed Ceratitis capi- diate in vivo germline transformation in two dipteran tata [6, 7], piggyBac from the cabbage looper moth, species, D. melanogaster and A. suspensa. Trichoplusia ni, that also initially transformed C. capi- tata [8, 9], and the Hermes element found in Musca Results domestica [10] used initially to transform Ae. aegypti Transformation experiments [11]. Hermes is a member of the hobo, Activator, Tam3 In the first of three transformation experiments we (hAT) family of transposons that has been found to be tested the hopperBd-we transposon vector system (now phylogenetically widespread [12]. While this supports referred to as hopper) in the D. melanogaster w[m] white the notion of widespread functionality, most full-length (eye) mutant host strain using the hopper vector, hAT elements (having a coding region and at least one pKhop[Dmwhite+], marked with the D. melanogaster terminal repeat sequence) were found to be defective, wild type mini-white+ gene. This serves as a transfor- and thus far none, other than Hermes, have been shown mant mutant-rescue marker by complementing the host − to support insect transformation. strain white mutation, resulting in eye pigmentation in Bd-Kah One of the defective hAT elements, hopper , was G1 germline transformants. The marker insertion within originally discovered by use of a short hAT-related PCR the transposase coding region creates a non- product as a hybridization probe to a lambda GEM12 autonomous vector that relies on an exogenous source genome library of the Kahuku wild type strain of the of transposase for transposition, that was provided by Oriental fruit fly, Bactrocera dorsalis [13]. The se- the pUChsHopper helper plasmid having the transposase quenced element was found to be 3120 bp in length with gene under D. melanogaster hsp70 promoter regulation 19 bp terminal inverted repeat (TIR) sequences with a for induction of expression by heat shock [17]. A mix- single mismatch. The TIRs surrounded a 1.9 kb consen- ture of vector and helper plasmids was injected into 436 sus hAT transposase transcriptional unit that was, how- dechorionated eggs under halocarbon oil, from which ever, interrupted by two frameshift mutations consistent 131 G0 adults survived (Table 1). A total of 70 adults with it being non-functional, in addition to a degenerate were backcrossed individually to w[m] adults, with an 8-bp genomic insertion site duplication. Southern blots additional 61 G0 adults mated in 28 groups of 2 to 3 to to genomic DNA from several B. dorsalis strains, and w[m] adults of the opposite sex, for a total of 98 G0 those from the melon fly, Zeugodacus cucurbitae, lines. Seventy-nine G0 fertile matings were screened for showed the presence of elements highly conserved with G1 progeny with pigmented eyes that were observed in hopperBd-Kah indicating the existence of related elements two of the matings, F11A and F23A (Fig. 1a), resulting in, and possibly beyond, the genus. in a transformation frequency of 2.5% per fertile G0. The In an effort to discover a functional paralog of hop- F11A G0 mating yielded three transformant progeny that Bd-Kah per ,5′ and 3′ primers to the hAT element were were considered to be G1 siblings resulting from the used in opposite orientation for inverse PCR in one of same transformation event. It is possible for marked G1 the other B. dorsalis strains carrying a white eye (we) siblings to arise from independent vector insertions, mutation and the presence of elements similar to hop- however all three lines shared the same female-specific perBd-Kah [14, 15]. This led to the discovery of a new marker phenotype that was mapped to the X- 3131 bp element in B. dorsalis, hopperBd-we. Unlike hop- chromosome in F11A, consistent with a common germ- perBd-Kah, hopperBd-we was found to have an uninter- line transformation event (see below). rupted 1950 bp reading frame, intact 19-bp TIR and 16- The second hopper transformation was similarly per- bp sub-TIR sequences, and a duplicated 8-bp insertion formed in the Drosophila w[m] strain, but using the Handler and Schetelig BMC Genetics 2020, 21(Suppl 2):137 Page 3 of 9 Table 1 hopperBd-we element transformation experiments in D. melanogaster and A. suspensa a b Host Vector G0 eggs injected G0s mated No. G0 lines No. fertile G0 lines No. G1 Transformation transformant lines frequencyc Dm pKhop [Dmwhite+] 436 131 98 79 2 0.025 Dm phop [PUb-DsRed.T3] 1056 203 170 129 2 0.016 As phop [PUb-DsRed.T3] 1453 389 103 94 9 0.096 aDm: D. melanogaster w[m] strain; As: A. suspensa wild type strain b + total number of G0 adults mated based on 70, 140, and 80 single G0 adult matings (to 3 opposite sex adults) for D. melanogaster pKhop[Dmwhite ] and phop[PUb-DsRed.T3] transformations, and the A. suspensa phop[PUb-DsRed.T3] transformation, respectively; additional G0s were mated in groups of 2–3 same sex G0 adults to opposite sex adults ctransformation frequency calculated as number of transformant lines per number of fertile lines phop[PUbDsRed.T3] vector, marked with a strongly ex- insertion sites could be identified and mapped by pressing fluorescent DsRed variant [18].
Load more

Recommended publications
  • Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia Pastoris
    www.nature.com/scientificreports OPEN Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia Received: 8 December 2017 Accepted: 19 June 2018 pastoris Published: xx xx xxxx Jinxiang Zhu1, Ruiqing Gong1, Qiaoyun Zhu1, Qiulin He1, Ning Xu1, Yichun Xu1, Menghao Cai1, Xiangshan Zhou1, Yuanxing Zhang1,2 & Mian Zhou1 In many prokaryotes but limited eukaryotic species, the combination of transposon mutagenesis and high-throughput sequencing has greatly accelerated the identifcation of essential genes. Here we successfully applied this technique to the methylotrophic yeast Pichia pastoris and classifed its conditionally essential/non-essential gene sets. Firstly, we showed that two DNA transposons, TcBuster and Sleeping beauty, had high transposition activities in P. pastoris. By merging their insertion libraries and performing Tn-seq, we identifed a total of 202,858 unique insertions under glucose supported growth condition. We then developed a machine learning method to classify the 5,040 annotated genes into putatively essential, putatively non-essential, ambig1 and ambig2 groups, and validated the accuracy of this classifcation model. Besides, Tn-seq was also performed under methanol supported growth condition and methanol specifc essential genes were identifed. The comparison of conditionally essential genes between glucose and methanol supported growth conditions helped to reveal potential novel targets involved in methanol metabolism and signaling. Our fndings suggest that transposon mutagenesis and Tn-seq could be applied in the methylotrophic yeast Pichia pastoris to classify conditionally essential/non-essential gene sets. Our work also shows that determining gene essentiality under diferent culture conditions could help to screen for novel functional components specifcally involved in methanol metabolism.
    [Show full text]
  • Evolutionary Dynamics of Hat DNA Transposon Families in Saccharomycetaceae
    GBE Evolutionary Dynamics of hAT DNA Transposon Families in Saccharomycetaceae Ve´ronique Sarilar1,2, Claudine Bleykasten-Grosshans3,andCe´cile Neuve´glise1,2,* 1INRA, UMR 1319 Micalis, Jouy-en-Josas, France 2AgroParisTech, UMR Micalis, Jouy-en-Josas, France 3CNRS, UMR 7156, Laboratoire de Ge´ne´tique Mole´culaire, Ge´nomique et Microbiologie, Universite´ de Strasbourg, Strasbourg, France *Corresponding author: E-mail: [email protected]. Accepted: December 6, 2014 Data deposition: This project has been deposited at EMBL-ENA under the accession LM651396-LM651399. Abstract Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium,andLachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis andinthesoleSaccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus.
    [Show full text]
  • Repeated Horizontal Transfers of Four DNA Transposons in Invertebrates and Bats Zhou Tang1†, Hua-Hao Zhang2†, Ke Huang3, Xiao-Gu Zhang2, Min-Jin Han1 and Ze Zhang1*
    Tang et al. Mobile DNA (2015) 6:3 DOI 10.1186/s13100-014-0033-1 RESEARCH Open Access Repeated horizontal transfers of four DNA transposons in invertebrates and bats Zhou Tang1†, Hua-Hao Zhang2†, Ke Huang3, Xiao-Gu Zhang2, Min-Jin Han1 and Ze Zhang1* Abstract Background: Horizontal transfer (HT) of transposable elements (TEs) into a new genome is considered as an important force to drive genome variation and biological innovation. However, most of the HT of DNA transposons previously described occurred between closely related species or insects. Results: In this study, we carried out a detailed analysis of four DNA transposons, which were found in the first sequenced twisted-wing parasite, Mengenilla moldrzyki. Through the homology-based strategy, these transposons were also identified in other insects, freshwater planarian, hydrozoans, and bats. The phylogenetic distribution of these transposons was discontinuous, and they showed extremely high sequence identities (>87%) over their entire length in spite of their hosts diverging more than 300 million years ago (Mya). Additionally, phylogenies and comparisons of transposons versus orthologous gene identities demonstrated that these transposons have transferred into their hosts by independent HTs. Conclusions: Here, we provided the first documented example of HT of CACTA transposons, which have been so far extensively studied in plants. Our results demonstrated that bats had continuously acquired new DNA elements via HT. This implies that predation on a large quantity of insects might increase bat exposure to HT. In addition, parasite-host interaction might facilitate exchanging of their genetic materials. Keywords: Horizontal transfer, CACTA transposons, Mammals, Recent activity Background or isolated species.
    [Show full text]
  • Evolutionary Dynamics of Hat DNA Transposon Families in Saccharomycetaceae Veronique Sarilar, Claudine Bleykasten-Grosshans, Cécile Neuvéglise
    Evolutionary Dynamics of hAT DNA Transposon Families in Saccharomycetaceae Veronique Sarilar, Claudine Bleykasten-Grosshans, Cécile Neuvéglise To cite this version: Veronique Sarilar, Claudine Bleykasten-Grosshans, Cécile Neuvéglise. Evolutionary Dynamics of hAT DNA Transposon Families in Saccharomycetaceae. Genome Biology and Evolution, Society for Molec- ular Biology and Evolution, 2015, 7 (1), pp.172-190. 10.1093/gbe/evu273. hal-01204467 HAL Id: hal-01204467 https://hal.archives-ouvertes.fr/hal-01204467 Submitted on 27 May 2020 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. GBE Evolutionary Dynamics of hAT DNA Transposon Families in Saccharomycetaceae Ve´ronique Sarilar1,2, Claudine Bleykasten-Grosshans3,andCe´cile Neuve´glise1,2,* 1INRA, UMR 1319 Micalis, Jouy-en-Josas, France 2AgroParisTech, UMR Micalis, Jouy-en-Josas, France 3CNRS, UMR 7156, Laboratoire de Ge´ne´tique Mole´culaire, Ge´nomique et Microbiologie, Universite´ de Strasbourg, Strasbourg, France *Corresponding author: E-mail: [email protected]. Accepted: December 6, 2014 Data deposition: This project has been deposited at EMBL-ENA under the accession LM651396-LM651399. Downloaded from Abstract Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction.
    [Show full text]
  • Identification of a High Frequency Transposon Induced By
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Genomics 93 (2009) 274–281 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Identification of a high frequency transposon induced by tissue culture, nDaiZ, a member of the hAT family in rice Jian Huang a,c, Kewei Zhang a,c, Yi Shen a,c, Zejun Huang a,c, Ming Li a, Ding Tang a, Minghong Gu b, Zhukuan Cheng a,⁎ a State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China b Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China c Graduate University of Chinese Academy of Sciences, Beijing 100049, China article info abstract Article history: Recent completion of rice genome sequencing has revealed that more than 40% of its genome consists of Received 14 July 2008 repetitive sequences, and most of them are related to inactive transposable elements. In the present study, a Accepted 14 November 2008 transposable element, nDaiZ0, which is induced by tissue culture with high frequency, was identified by Available online 23 December 2008 sequence analysis of an allelic line of the golden hull and internode 2 (gh2) mutant, which was integrated into the forth exon of GH2. The 528-bp nDaiZ0 has 14-bp terminal inverted repeats (TIRs), and generates an 8-bp Keywords: duplication of its target sites (TSD) during its mobilization.
    [Show full text]
  • Transposition of Hat Elements Links Transposable Elements and V(D)J Recombination
    articles Transposition of hAT elements links transposable elements and V(D)J recombination Liqin Zhou1, Rupak Mitra1, Peter W. Atkinson2, Alison Burgess Hickman3, Fred Dyda3 & Nancy L. Craig1 1Howard Hughes Medical Institute and Department of Molecular Biology & Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA 2Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA 3Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA ........................................................................................................................................................................................................................... Transposons are DNA sequences that encode functions that promote their movement to new locations in the genome. If unregulated, such movement could potentially insert additional DNA into genes, thereby disrupting gene expression and compromising an organism’s viability. Transposable elements are classified by their transposition mechanisms and by the transposases that mediate their movement. The mechanism of movement of the eukaryotic hAT superfamily elements was previously unknown, but the divergent sequence of hAT transposases from other elements suggested that these elements might use a distinct mechanism. Here we have analysed transposition of the insect hAT element Hermes in vitro. Like other transposons, Hermes excises from DNA
    [Show full text]
  • Transposon-Induced Gene Activation As a Mechanism Generating Cluster Shape Somatic Variation in Grapevine
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC The Plant Journal (2010) 61, 545–557 doi: 10.1111/j.1365-313X.2009.04090.x Transposon-induced gene activation as a mechanism generating cluster shape somatic variation in grapevine Lucie Fernandez1,2, Laurent Torregrosa3, Vincent Segura4, Alain Bouquet3,† and Jose´ M. Martinez-Zapater1,2,* 1Departmento de Gene´ tica Molecular de Plantas, Centro Nacional de Biotecnologı´a, CSIC, C/Darwin 3, 28049 Madrid, Spain, 2Instituto de Ciencias de la Vid y del Vino (ICVV), (CSIC, Universidad de La Rioja, Gobierno de La Rioja), CCT, Campus de la Universidad de La Rioja, C/Madre de Dios 51, 26006 Logron˜ o, Spain, 3INRA-SupAgro, UMR DIA-PC, Campus SupAgro/INRA, 2 Place P. Viala, 34060 Montpellier Cedex, France, and 4Department of Biology, Centre for Novel Agricultural Products, University of York, PO Box 373, York YO10 5YW, UK Received 12 August 2009; revised 17 October 2009; accepted 2 November 2009; published online 4 January 2010. *For correspondence (fax + 34 915854506; e-mail [email protected]). †Our friend and colleague Alain Bouquet, who actively participated in this work and co-authored this manuscript, passed away unexpectedly during its final writing. He enjoyed a very productive scientific life, dedicated to the biology of grapevine and its genetic improvement, and he was an enthusiastic and wonderful person, professor and colleague. We dedicate this article to his memory. SUMMARY We have characterized the genetic and molecular origin of the reiterated reproductive meristem (RRM) somatic variant phenotype of grapevine cultivar Carignan.
    [Show full text]
  • Transposon-Induced Inversions Activate Gene Expression in Maize Pericarp
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.08.434479; this version posted March 9, 2021. 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. 1 Transposon-induced inversions activate gene expression in Maize pericarp 2 Sharu Paul Sharma*, Tao Zuo* and Thomas Peterson*† 3 * Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 4 50011 5 † Department of Agronomy, Iowa State University, Ames, IA 50011 6 7 Abstract 8 Chromosomal inversions can have considerable biological and agronomic impacts including 9 disrupted gene function, change in gene expression and inhibited recombination. Here we 10 describe the molecular structure and functional impact of six inversions caused by Alternative 11 Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize 12 line p1-wwB54, the p2 gene is expressed in anther and silk but not in pericarp, making the 13 kernels white. We identified inversions in this region caused by transposition of Ac and fractured 14 Ac (fAc) transposable elements. These inversions change the position of a p1 enhancer and 15 activate the expression of p2 in the kernel pericarp, resulting in red kernel color. We hypothesize 16 that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 17 expression in kernel pericarp. 18 19 20 21 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.08.434479; this version posted March 9, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution
    Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution by Tyler Adam Elliott A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Integrative Biology Guelph, Ontario, Canada © Tyler Adam Elliott, December, 2016 ABSTRACT Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution Tyler Adam Elliott Advisor: University of Guelph, 2016 Professor T.R. Gregory Transposable elements (TEs), mobile pieces of self-replicating DNA, are one of the driving forces behind genomic evolution in eukaryotic organisms. Their contribution to genome size variation and as mutagens has led researchers to pursue their study in the hope of better understanding the evolution of genomic properties and organismal phenotypes But TEs can also be thought of in a multi-level evolutionary context, with TEs best understood as evolving populations residing within (and interacting with) the host genome. I argue, with empirical evidence from the literature, that the multi-level approach advocated by the classic ―selfish DNA‖ papers of 1980 has become less commonly invoked over the past 35 years, in a favour of a strictly organism-centric view. I also make the case that an exploration of evolution at the level of TEs within genomes is required, one which articulates the similarities and differences between a TE population and a traditional population of organisms. A comprehensive analysis of sequenced eukaryote genomes outlines the landscape of how TE superfamilies are distributed, but also reveals that how TEs are reported needs to be addressed. A proper exploration of evolution at the TE level will require a dramatic change to how TE information is annotated, curated, and stored, and I make several specific recommendations in this regard.
    [Show full text]
  • Genome Rearrangement at Reversed-Ends Ds Element in Arabidopsis Lakshminarasimhan Krishnaswamy Iowa State University
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2007 Genome rearrangement at reversed-ends Ds element in Arabidopsis Lakshminarasimhan Krishnaswamy Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Genetics and Genomics Commons, and the Molecular Biology Commons Recommended Citation Krishnaswamy, Lakshminarasimhan, "Genome rearrangement at reversed-ends Ds element in Arabidopsis" (2007). Retrospective Theses and Dissertations. 15969. https://lib.dr.iastate.edu/rtd/15969 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genome rearrangement at reversed-ends Ds element in Arabidopsis by Lakshminarasimhan Krishnaswamy A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Physiology Program of Study Committee: Thomas Peterson, Major Professor Jack Girton Martin Spalding Daniel Voytas Steven Whitham Iowa State University Ames, Iowa 2007 Copyright © Lakshminarasimhan Krishnaswamy, 2007. All rights reserved. UMI Number: 3259493 UMI Microform 3259493 Copyright 2007 by ProQuest Information and Learning Company. All rights reserved.
    [Show full text]
  • Exploring the Functional Landscape of the Fission Yeast Genome Via Hermes Transposon Mutagenesis
    Exploring the Functional Landscape of the Fission Yeast Genome via Hermes Transposon Mutagenesis Leanne Grech Submitted for the Degree of Doctor of Philosophy (PhD) University College London Primary Supervisor: Professor Jürg Bähler (UCL) January 2018 1 Declaration “I, Leanne Grech, confirm that the work presented in this thesis is my own, and where information has been derived from other sources, I confirm that this has been indicated in the thesis.” 2 Abstract In general, the non-protein-coding dark matter of eukaryotic genomes remains poorly understood. Neither diversity studies, comparative genomics, nor the biochemical outputs allow fine-scale descriptions of the genomic elements that are required for an organism to grow. Transposon mutagenesis offers an alternative approach to locate functional regions. In principle, insertion mutants are created in large pools, and mutants harbouring harmful insertions are quantitatively removed from the population. Subsequent sequencing of mutant libraries should reveal functionality in regions with fewer insertions. Transposon mutagenesis works well in bacteria. We applied the Hermes transposon system to locate functional regions in the Schizosaccharomyces pombe, or fission yeast genome. We created multiple dense insertion libraries, during log phase growth and chronological ageing, achieving a saturating (or near-saturating) insertion density of 1 insertion per 13 nucleotides of the genome for log phase samples. To account for the complexity and stochastic nature of the data, we applied a five-state hidden Markov model (HMM) that includes generalised linear models to account for systematic insertion biases (e.g. nucleosomes). The HMM state provides a semi-quantitative estimate of the functional significance of the genome at single nucleotide-level resolution.
    [Show full text]
  • Multiple Waves of Recent DNA Transposon Activity in the Bat, Myotis Lucifugus
    Letter Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus David A. Ray,1,5,6 Cedric Feschotte,2,5 Heidi J.T. Pagan,1 Jeremy D. Smith,1 Ellen J. Pritham,2 Peter Arensburger,3 Peter W. Atkinson,3 and Nancy L. Craig4 1Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA; 2Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA; 3Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA; 4Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and Helitron elements, two distinct groups of DNA transposons, in the lineage of the vespertilionid bat Myotis lucifugus. Here, we describe seven additional families that have also been recently active in the bat lineage. Early vespertilionid genome evolution was dominated by the activity of Helitrons, mariner-like and Tc2-like elements. This was followed by the colonization of Tc1-like elements, and by a more recent explosion of hAT-like elements. Finally, and most recently, piggyBac-like elements have amplified within the Myotis genome and our results indicate that one of these families is probably still expanding in natural populations. Together, these data suggest that there has been tremendous recent activity of various DNA transposons in the bat lineage that far exceeds those previously reported for any mammalian lineage.
    [Show full text]