DOCSLIB.ORG

Interspecific DNA Transformation in Drosophila (Drosophila Melanogaster/Drosophila Simulans/Rosy Gene/P Element/Transposable Element) NANCY J

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Interspecific DNA Transformation in Drosophila (Drosophila Melanogaster/Drosophila Simulans/Rosy Gene/P Element/Transposable Element) NANCY J Proc. Nati. Acad. Sci. USA Vol. 81, pp. 7515-7519, December 1984 Genetics Interspecific DNA transformation in Drosophila (Drosophila melanogaster/Drosophila simulans/rosy gene/P element/transposable element) NANCY J. SCAVARDA AND DANIEL L. HARTL Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110 Communicated by Peter H. Raven, August 7, 1984 ABSTRACT A DNA fragment that includes the wild-type (4). Use of an average rate of synonymous substitutions in rosy (ry+) gene of Drosophila melanogaster has been intro- coding regions of 5.1 + 0.3 x 10-9 per nucleotide site per yr duced by microinjection into the germ line of the reproductive- (9, 10) results in an estimated time since separation of 4.1 + ly isolated species Drosophila simulans and incorporated into 0.2 million yr, but analogous estimates based on rates of nu- the D. simulans genome. Transformation was mediated by the cleotide substitution in intervening sequences range from 3.8 transposable element P, which occurs in the genome of most to 6.8 million yr. These estimates are uncertain because av- natural populations ofD. melanogaster but not in D. simulans. erage rates of substitution in other organisms may have little Rubin and Spradling [Rubin, G. M. & Spradling, A. C. relevance to insects, and because evolutionary change in the (1982) Science 218, 348-353] have previously shown that the gene coding for alcohol dehydrogenase may be atypical. ry' DNA fragment, which is flanked by recognition sequences Although D. melanogaster and D. simulans are reproduc- of P element, can transform the germ line ofD. melanogaster. tively isolated, the species can be hybridized. Indeed, D. Successful transformation in D. simulans indicates that the P simulans was first recognized as a group of strains that pro- element continues to function as a transposable element in the duced nearly unisexual progeny in crosses with D. melano- D. simulans genome. Moreover, the ry' gene ofD. melanogas- gaster (11). However, interspecific mating is difficult to ter functions in the genome of D. simulans to produce normal achieve even under laboratory conditions, and most of the eye color, despite the estimated 1 to 5 million yr of reproduc- hybrids that survive are of the same sex as their D. melano- tive isolation since the evolutionary divergence of these species. gaster parent (11, 12). Interspecific hybrids usually have re- Interspecific DNA transformation provides a useful method duced viability, and they are invariably sterile (13, 14). The for the study of genetic differences affecting gene expression cross of triploid D. melanogaster with heavily irradiated D. among related but reproductively isolated species. simulans results in offspring having various combinations of chromosomes from the parental species, but virtually all of Drosophila melanogaster Meigen (1830) and Drosophila the hybrids are sterile (15). simulans Sturtevant (1929) are sibling species in the subge- The sterility of the hybrids between D. melanogaster and nus Sophophora, which together with six other described D. simulans and their reduced viability undoubtedly results species form the melanogaster species subgroup. The pres- in part from the fixation of genetic differences between the ent biogeographical distribution of the subgroup implies that species that accompanied the process of speciation 1-5 mil- it almost certainly originated and diversified in Africa (1, 2). lion yr ago and in part from genetic differences that have D. melanogaster and D. simulans are morphologically near- accumulated since that time. To study genetic differences ly indistinguishable except for the male genitalia, and their between related but reproductively isolated species, it would only major karyotypic difference is in a large inversion in the be useful to have a method for transferring individual genes right arm of the third chromosome (3). Both species are cos- between them. As Muller and Pontecorvo pointed out long mopolitan in distribution and often exist sympatrically, but ago (15), "the genetic analysis of species differences is of they are completely isolated reproductively. especial interest in precisely those cases where the sterility The time elapsed since the evolutionary separation of D. or inviability of the hybrids between the species stands in the melanogaster and D. simulans is very uncertain. One esti- way of such analysis." mate (4) is based on a comparison of the genetic distance A method of DNA-mediated transformation of germ cells between the species in terms of electrophoretically detected of D. melanogaster has recently been developed that uses enzyme differences (5, 6) and the rate at which genetic dis- the transposase enzyme of a transposable element (P ele- tance has accumulated in the planitibia subgroup of Hawai- ment) to catalyze the transposition of a genetically engi- ian drosophilids, which is known because of the exceptional- neered element consisting of the DNA sequence of interest ly well understood geological history ofthe Hawaiian Islands flanked by the recognition sequences of P element (16-20). (7). This estimate is 0.8 + 0.2 million yr, but the estimate is We have investigated whether this system of intraspecific of uncertain validity because it is based on the rate ofgenetic transformation can successfully catalyze interspecific trans- divergence in a distantly related subgroup of species, which formation between D. melanogaster and D. simulans. The may have evolved at an unusually rapid rate because of the result is that interspecific transformation does occur, which island habitat; it is also uncertain because substantial genetic implies that the P element also functions as a transposable divergence occurs among local populations of D. melano- element when present in the germ cells of D. simulans. This gaster (8). Much greater times since separation are estimated the for from of differences in nucleotide sequence be- finding has implications regarding potential transpos- comparison able elements such as the P element to be disseminated tween the D. melanogaster and D. simulans gene coding for the alcohol dehydrogenase and the average rate of nucleotide across interspecific reproductive barriers. Moreover, substitution that occurs among genes in other organisms method of interspecific gene transfer will be ofgeneral use in whose evolutionary history is known from the fossil record studies of the molecular biology and evolution of gene regu- lation in related but reproductively isolated species of Dro- The publication costs of this article were defrayed in part by page charge sophila. payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. Abbreviation: kb, kilobase(s). 7515 Downloaded by guest on September 23, 2021 7516 Genetics: Scavarda and Hartl Proc. Natl. Acad ScL USA 81 (1984) MATERIALS AND METHODS pH 8.0). After extraction with phenol and with chloroform/ isoamyl alcohol (25:1), the DNA was precipitated as de- Recovery of a rosy (ry) Mutation in D. simulans. A strain of scribed above and resuspended in 20 dul of buffer A. D. simulans carrying a vermilion (v) mutation was provided Restriction endonuclease digests were carried out accord- by Victoria Finnerty. Males of this strain were subjected to ing to supplier's instructions with 20 units of enzyme in a mutagenesis with ethyl methanesulfonate (21) prior to mat- final vol of 50 td. Samples were subjected to overnight elec- ing with v females. Approximately 300 F1 offspring from trophoresis at 40 V in 0.7% agarose gels in 40 mM Tris ace- treated males were mated individually with v females, and tate/2 mM EDTA, pH 8.0, and were stained with ethidium the F2 offspring were sib-mated. The resulting F3 progeny bromide. were screened for orange-eyed flies (the v ry double mutant DNA Hybridization. Transfer of DNA to nitrocellulose fil- has orange eyes), and two putative ry mutants were recov- ters (Schleicher & Schuell BA85) and hybridization at 650C ered. One of these was identified as a ry mutation because it was carried out as described (25). Fragments used as probes failed to complement a known ry mutation in interspecific were isolated by a modification of the glass powder method hybrids with D. melanogaster. The mutation was also found (26) and nick-translated with [a-32P]dATP (New England to lack xanthine dehydrogenase activity, the gene product of Nuclear) to a specific activity of >108 (27). ry. The v ry strain was freed of the v mutation by crossing dpm//ig with wild-type D. simulans followed by inbreeding to reex- RESULTS tract the ry mutation. The resulting strain was designated iso-1, and the ry mutation in this strain was designated ry83. Identification of ry Mutation in D. simuians. Fig. 1 shows a Protein Electrophoresis. Extracts of individual flies were protein electrophoresis polyacrylamide gel stained for xan- subjected to electrophoresis in 7% polyacrylamide gels with thine dehydrogenase, the gene product of the ry locus. The 40 mM Tris glycine buffer (pH 8.3) at 150 V for 4.5 hr. Gels indicated lanes contain protein extracts of ry0 [a D. mela- were stained for xanthine dehydrogenase in 100 mM nogaster strain carrying a deletion of part of the ry locus (17)], wild-type D. simulans, the D. simulans strain iso-1, and Tris HCl, pH 7.1/0.7 uM phenazine methosulfate/5 u.M wild-type D. melanogaster. Based on the absence of detect- NAD+/2 ,tM nitro blue tetrazolium/7 uM hypoxanthine. able xanthine dehydrogenase activity in the iso-1 strain and Transformation. Transformation mediated by the P ele- the inability of the mutation in this strain to complement a ment was carried out as described by Rubin and Spradling known ry mutation in interspecific hybrids with D. melano- (16, 17). The injected DNA solution contained plasmid Car- gaster, we conclude that the mutation in iso-1 is in the ry negie-20 (300 jig/ml), which carries a 7.2-kilobase (kb) frag- locus, and we designate the mutation as ryi83.
Load more

Recommended publications
  • Copy Number of P Elements, KP/Full-Sized P Element Ratio and Their Relationships with Environmental Factors in Brazilian Drosophila Melanogaster Populations
    Heredity (2003) 91, 570–576 & 2003 Nature Publishing Group All rights reserved 0018-067X/03 $25.00 www.nature.com/hdy Copy number of P elements, KP/full-sized P element ratio and their relationships with environmental factors in Brazilian Drosophila melanogaster populations MT Ruiz and CMA Carareto Departamento de Biologia, IBILCE, Universidade Estadual Paulista, Rua Cristo´va˜o Colombo, 2265, Jardim Nazare´,Sa˜o Jose´ do Rio Preto 15054-000, SP, Brazil The P transposable element copy numbers and the KP/full- and the strains from less extreme latitudes had many sized P element ratios were determined in eight Brazilian more full-sized P than KP elements. However, no clinal strains of Drosophila melanogaster. Strains from tropical variation was observed. Strains from different localities, regions showed lower overall P element copy numbers previously classified as having P cytotype, displayed a higher than did strains from temperate regions. Variable numbers of or a lower proportion of KP elements than of full-sized full-sized and defective elements were detected, but the P elements, as well as an equal number of the two element full-sized P and KP elements were the predominant classes types, showing that the same phenotype may be produced of elements in all strains. The full-sized P and KP element by different underlying genomic components of the P–M ratios were calculated and compared with latitude. The system. northernmost and southernmost Brazilian strains showed Heredity (2003) 91, 570–576, advance online publication, fewer full-sized elements than KP elements per genome, 17 September 2003; doi:10.1038/sj.hdy.6800360 Keywords: P transposable elements; KP elements; KP/full-sized P elements; P–M systems; Drosophila melanogaster Introduction elements, allows P element transposition (Engels, 1983).
    [Show full text]
  • Evolution of Pogo, a Separate Superfamily of IS630-Tc1-Mariner
    Gao et al. Mobile DNA (2020) 11:25 https://doi.org/10.1186/s13100-020-00220-0 RESEARCH Open Access Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates Bo Gao, Yali Wang, Mohamed Diaby, Wencheng Zong, Dan Shen, Saisai Wang, Cai Chen, Xiaoyan Wang and Chengyi Song* Abstracts Background: Tc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood. Results: Here, phylogenetic analysis show that pogo transposases, together with Tc1/mariner,DD34E/Gambol,and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover,andFot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals—even mammals—and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix–turn–helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2–7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events.
    [Show full text]
  • Genome of Drosophila Guanche WOLFGANG J
    Proc. Nati. Acad. Sci. USA Vol. 89, pp. 4018-4022, May 1992 Genetics P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche WOLFGANG J. MILLER*, SYLVIA HAGEMANNt, ELEONORE REITERt, AND WILHELM PINSKERtt *Institut fur Botanik, Abteilung Cytologie und Genetik, Rennweg 14, A-1030 Vienna, Austria; and tInstitut fur Allgemeine Biologie, Abteilung Genetik, Wahringerstrasse 17, A-1090 Vienna, Austria Communicated by Bruce Wallace, December 23, 1991 ABSTRACT In Drosophila guanche, P-homologous se- In germ-line cells, the copy number of P elements is quences were found to be located in a tandem repetitive array genetically regulated by a complex mixture of chromosomal (copy number: 20-50) at a single genomic site. The cytological and cytoplasmic factors (11). At least two mechanisms can be position on the polytene chromosomes was determined by in situ distinguished: the maternally transmitted cytotype (12) and a hybridization (chromosome 0: 85C). Sequencing of one com- chromosomally inherited control system (13). In the P cyto- plete repeat unit (3.25 kilobases) revealed high sequence simi- type, the cytoplasmic state of P-strain individuals, transpo- larity between the central coding region comprising exons 0 to sition is repressed in somatic cells and in the germ line. In 2 and the corresponding section of the Drosophila melanogaster general the P cytotype develops gradually as a result of the P element. The rest of the sequence has diverged considerably. increasing number of P-element copies. M-strains, on the Exon 3 has no coding function and the inverted repeats have other hand, have genomes devoid of P elements.
    [Show full text]
  • History to the Rescue Pseudogenes Get Some Respect Flyin' Pain Free
    RESEARCH NOTES Pseudogenes get some respect adenoviral entry is mediated by interaction between RGD motifs and integrins, they went on to engineer a virus with an RGD peptide. This Pseudogenes are the non-functional remnants of genes that have version of the modified virus specifically infected tumor cells and repli- been thought to do nothing more than take up space. A new cated more effectively than Delta-24. When injected directly into report by Shinji Hirotsune and colleagues provides evidence that human gliomas xenografted into mice, Delta-24-RGD allowed signifi- at least one such pseudogene has an essential role as a regulator of cantly longer survival than did Delta-24 or an inactivated virus control. gene expression (Nature 423, 91–96; 2003). A fortuitous insertion More impressively, 60% of mice treated with Delta-24-RGD were long- of a transgene into the Makorin1-p1 locus generated a mouse term survivors (compared with 15% of those treated with Delta-24 with a bone deformity and polycystic kidneys. Makorin1-p1 is a characterized by complete tumor regression). MH pseudogene that is normally transcribed, although no functional protein product can be produced. Strikingly, the transgene insertion reduced not only the transcription of Makorin1-p1, but RNAi on or off target? that of its functional homolog, Makorin1, as well. In vitro Two new reports examine the specificity of RNA interference (RNAi) in experiments show that an intact Makorin1-p1 locus stabilizes the human cells using genome-wide expression profiling. Targeting exoge- Makorin1 mRNA, and a rescue of the original transgenic mouse nous GFP in human embryonic kidney cells, Jen-Tsan Chi and col- with Makorin1-p1 proves that the pseudogene is required for leagues report efficient and specific knockdown using two different normal expression of Makorin1.
    [Show full text]
  • Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using White Co-Conversion
    G3: Genes|Genomes|Genetics Early Online, published on August 26, 2016 as doi:10.1534/g3.116.032557 Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using white Co-Conversion Daniel Tianfang Ge*,†,1, Cindy Tipping*,‡,1, Michael H. Brodsky§, Phillip D. Zamore*,‡,**,2 *RNA Therapeutics Institute, †Interdisciplinary Graduate Program, ‡Howard Hughes Medical Institute, §Department of Molecular, Cell and Cancer Biology, **Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA 1These authors contributed equally to this work. 2To whom correspondence should be addressed. 1 © The Author(s) 2013. Published by the Genetics Society of America. Running title: Rapid Screening for CRISPR Editing Keywords: Cas9; Co-Conversion; Genetic Screen; Microhomology-Mediated End Joining; Homologous Recombination Corresponding author: Phillip D. Zamore Address: 368 Plantation Street, AS4-2053, Worcester, MA 01605 Tel.: 508-856-2191 E-mail: [email protected] 2 1 ABSTRACT 2 Adoption of a streamlined version of the bacterial CRISPR/Cas9 defense system has 3 accelerated targeted genome engineering. The Streptococcus pyogenes Cas9 protein, 4 directed by a simplified, CRISPR-like single guide RNA, catalyzes a double-stranded 5 DNA break at a specific genomic site; subsequent repair by end joining can introduce 6 mutagenic insertions or deletions, while repair by homologous recombination using an 7 exogenous DNA template can incorporate new sequence at the target locus. However, 8 the efficiency of Cas9-directed mutagenesis is low in Drosophila melanogaster. Here, we 9 describe a strategy that reduces the time and effort required to identify flies with 10 targeted genomic changes.
    [Show full text]
  • Evaluating the Probability of CRISPR-Based Gene Drive Contaminating Another Species
    bioRxiv preprint doi: https://doi.org/10.1101/776609; this version posted September 19, 2019. 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 4.0 International license. Evaluating the Probability of CRISPR-based Gene Drive Contaminating Another Species 1 2 3 4 Virginie Courtier-Orgogozo ,​ Antoine Danchin ,​ Pierre-Henri Gouyon ​ and Christophe Boëte ​ ​ ​ ​ 1 I​ nstitut Jacques Monod, CNRS, UMR 7592, Université de Paris, Paris, France 2 I​ nstitut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris Descartes, Paris, France 3 I​ nstitut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France 4 I​ SEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France Abstract The probability D that a given CRISPR-based gene drive element contaminates another, non-target species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = (hyb+transf).express.cut.flank.immune.nonextinct with ​ ​ hyb = probability of hybridization between the target species and a non-target species ​ transf = probability of horizontal transfer of a piece of DNA containing the gene drive ​ cassette from the target species to a non-target species (with no hybridization) express = probability that the Cas9 and guide RNA genes are expressed ​ ​ ​ cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the ​ new host flank = probability that the gene drive cassette inserts at the cut site ​ immune = probability that the immune system does not reject Cas9-expressing cells ​ ​ ​ nonextinct = probability of invasion of the drive within the population ​ We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans.
    [Show full text]
  • A Review on the Population Genomics of Transposable Elements
    G C A T T A C G G C A T genes Review On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements Yann Bourgeois and Stéphane Boissinot * New York University Abu Dhabi, P.O. 129188 Saadiyat Island, Abu Dhabi, UAE; [email protected] * Correspondence: [email protected] Received: 4 April 2019; Accepted: 21 May 2019; Published: 30 May 2019 Abstract: Transposable elements (TEs) play an important role in shaping genomic organization and structure, and may cause dramatic changes in phenotypes. Despite the genetic load they may impose on their host and their importance in microevolutionary processes such as adaptation and speciation, the number of population genetics studies focused on TEs has been rather limited so far compared to single nucleotide polymorphisms (SNPs). Here, we review the current knowledge about the dynamics of transposable elements at recent evolutionary time scales, and discuss the mechanisms that condition their abundance and frequency. We first discuss non-adaptive mechanisms such as purifying selection and the variable rates of transposition and elimination, and then focus on positive and balancing selection, to finally conclude on the potential role of TEs in causing genomic incompatibilities and eventually speciation. We also suggest possible ways to better model TEs dynamics in a population genomics context by incorporating recent advances in TEs into the rich information provided by SNPs about the demography, selection, and intrinsic properties of genomes. Keywords: transposable elements; population genetics; selection; drift; coevolution 1. Introduction Transposable elements (TEs) are repetitive DNA sequences that are ubiquitous in the living world and have the ability to replicate and multiply within genomes.
    [Show full text]
  • The Evolutionary Life History of P Transposons: from Horizontal Invaders to Domesticated Neogenes
    Chromosoma (2001) 110:148–158 DOI 10.1007/s004120100144 CHROMOSOMA FOCUS Wilhelm Pinsker · Elisabeth Haring Sylvia Hagemann · Wolfgang J. Miller The evolutionary life history of P transposons: from horizontal invaders to domesticated neogenes Received: 5 February 2001 / In revised form: 15 March 2001 / Accepted: 15 March 2001 / Published online: 3 May 2001 © Springer-Verlag 2001 Abstract P elements, a family of DNA transposons, are uct of their self-propagating lifestyle. One of the most known as aggressive intruders into the hitherto uninfected intensively studied examples is the P element of Dro- gene pool of Drosophila melanogaster. Invading through sophila, a family of DNA transposons that has proved horizontal transmission from an external source they useful not only as a genetic tool (e.g., transposon tag- managed to spread rapidly through natural populations ging, germline transformation vector), but also as a model within a few decades. Owing to their propensity for rapid system for investigating general features of the evolu- propagation within genomes as well as within popula- tionary behavior of mobile DNA (Kidwell 1994). P ele- tions, they are considered as the classic example of self- ments were first discovered as the causative agent of hy- ish DNA, causing havoc in a genomic environment per- brid dysgenesis in Drosophila melanogaster (Kidwell et missive for transpositional activity. Tracing the fate of P al. 1977) and were later characterized as a family of transposons on an evolutionary scale we describe differ- DNA transposons
    [Show full text]
  • CRISPR/Cas9 and Genome Editing in Drosophila*
    Available online at www.sciencedirect.com ScienceDirect JGG Journal of Genetics and Genomics 41 (2014) 7e19 REVIEW CRISPR/Cas9 and Genome Editing in Drosophila* Andrew R. Bassett*, Ji-Long Liu* MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, United Kingdom Received 25 November 2013; revised 10 December 2013; accepted 11 December 2013 Available online 18 December 2013 ABSTRACT Recent advances in our ability to design DNA binding factors with specificity for desired sequences have resulted in a revolution in genetic engineering, enabling directed changes to the genome to be made relatively easily. Traditional techniques for generating genetic mutations in most organisms have relied on selection from large pools of randomly induced mutations for those of particular interest, or time-consuming gene targeting by homologous recombination. Drosophila melanogaster has always been at the forefront of genetic analysis, and application of these new genome editing techniques to this organism will revolutionise our approach to performing analysis of gene function in the future. We discuss the recent techniques that apply the CRISPR/Cas9 system to Drosophila, highlight potential uses for this technology and speculate upon the future of genome engineering in this model organism. KEYWORDS: Drosophila melanogaster; CRISPR; Cas9; Genome engineering; Targeted mutagenesis INTRODUCTION mutagenise or alter gene function in a desired manner (Rong and Golic, 2000), the difficulty of applying these techniques The advent of genome sequencing and genome-wide on a large scale has restricted our ability to test hypotheses technologies for study of gene expression, polymorphism generated from such genome-wide analyses.
    [Show full text]
  • Genetic Evidence for Adaptation-Driven Incipient Speciation of Drosophila Melanogaster Along a Microclimatic Contrast in ‘‘Evolution Canyon,’’ Israel
    Genetic evidence for adaptation-driven incipient speciation of Drosophila melanogaster along a microclimatic contrast in ‘‘Evolution Canyon,’’ Israel Pawel Michalak*†, Irina Minkov†, Amanda Helin*, Daniel N. Lerman*, Brian R. Bettencourt*, Martin E. Feder*, Abraham B. Korol†, and Eviatar Nevo†‡ *Department of Organismal Biology and Anatomy, University of Chicago, 1027 East 57th Street, Chicago, IL 60637-1508; and †Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel Contributed by Eviatar Nevo, September 11, 2001 Substantial genetic differentiation, as great as among species, (16–18). We thus ask: Have the populations likewise diverged exists between populations of Drosophila melanogaster inhabiting genetically according to microsatellite markers and a candidate opposite slopes of a small canyon. Previous work has shown that gene strongly linked to resistance to environmental stress? Is this prezygotic sexual isolation and numerous differences in stress- divergence consistent with genetic isolation despite the conti- related phenotypes have evolved between D. melanogaster pop- guity of the D. melanogaster populations in the canyon? Finally, ulations in ‘‘Evolution Canyon,’’ Israel, in which slopes 100–400 m does the divergence implicate any evolutionary mechanism(s) as apart differ dramatically in aridity, solar radiation, and associated its cause? vegetation. Because the canyon’s width is well within flies’ dis- To address these questions, we analyzed both putatively persal capabilities, we examined genetic changes associated with neutral (microsatellites) and non-neutral (hsp70Ba, a heat shock local adaptation and incipient speciation in the absence of geo- gene) markers in D. melanogaster collected from the middle EVOLUTION graphical isolation. Here we report remarkable genetic differenti- elevation of each slope.
    [Show full text]
  • Drosophila IRBP Bzip Heterodimer Binds P-Element DNA and Affects Hybrid Dysgenesis
    Drosophila IRBP bZIP heterodimer binds P-element DNA and affects hybrid dysgenesis Malik Joseph Francisa, Siobhan Rochea, Michael Jeffrey Choa, Eileen Bealla, Bosun Mina, Ronaldo Paolo Panganibana, and Donald C. Rioa,b,c,1 aDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; bCenter for RNA Systems Biology, University of California, Berkeley, CA 94720; and cCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 Edited by Nancy L. Craig, Johns Hopkins University School of Medicine, Baltimore, MD, and approved October 3, 2016 (received for review August 12, 2016) In Drosophila, P-element transposition causes mutagenesis and remain tightly bound by the transposase enzyme (10, 16). The genome instability during hybrid dysgenesis. The P-element flanking donor site DNA is released after P-element cleavage 31-bp terminal inverted repeats (TIRs) contain sequences essential (16) and needs to be efficiently repaired by endogenous DNA for transposase cleavage and have been implicated in DNA repair repair mechanisms. Engineered somatic mobilization of as few via protein–DNA interactions with cellular proteins. The identity and as 15–20 small nonautonomous P elements by transposase leads function of these cellular proteins were unknown. Biochemical char- to a temperature-dependent pupal lethality due to extensive acterization of proteins that bind the TIRs identified a heterodimeric DNA damage and apoptosis (17). basic leucine zipper (bZIP) complex between an uncharacterized pro- Repair of P-element–induced DNA breaks typically occurs tein that we termed “Inverted Repeat Binding Protein (IRBP) 18” and through two distinct DSB repair pathways: nonhomologous end its partner Xrp1. The reconstituted IRBP18/Xrp1 heterodimer binds joining (NHEJ) or a variant of classical homologous recombinational sequence-specifically to its dsDNA-binding site within the P-element repair, termed “Synthesis-Dependent Strand Annealing” (SDSA) TIRs.
    [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]