Transposable Elements and Genome Size Dynamics in Gossypium Jennifer S
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Specificity of Genome Evolution in Experimental Populations Of
Specificity of genome evolution in experimental PNAS PLUS populations of Escherichia coli evolved at different temperatures Daniel E. Deatheragea,b,c,d, Jamie L. Kepnera,b,c,d, Albert F. Bennette, Richard E. Lenskif,g,1, and Jeffrey E. Barricka,b,c,d,f,1 aCenter for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712; bCenter for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712; cInstitute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712; dDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712; eDepartment of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697; fBEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824; and gDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 Edited by Neil H. Shubin, The University of Chicago, Chicago, IL, and approved January 25, 2017 (received for review September 27, 2016) Isolated populations derived from a common ancestor are expected to produce only in environments within a restricted thermal range. diverge genetically and phenotypically as they adapt to different local Adaptation for improved thermotolerance has important impli- environments. To examine this process, 30 populations of Escherichia cations for plant growth (5) and crop productivity (6), especially coli were evolved for 2,000 generations, with six in each of five dif- in light of climate change (7). Directed evolution of microor- ferent thermal regimes: constant 20 °C, 32 °C, 37 °C, 42 °C, and daily ganisms, such as yeast, to function effectively at higher or lower alternations between 32 °C and 42 °C. -
Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus
Genome analysis of the smallest free-living eukaryote SEE COMMENTARY Ostreococcus tauri unveils many unique features Evelyne Derellea,b, Conchita Ferrazb,c, Stephane Rombautsb,d, Pierre Rouze´ b,e, Alexandra Z. Wordenf, Steven Robbensd, Fre´ de´ ric Partenskyg, Sven Degroeved,h, Sophie Echeynie´ c, Richard Cookei, Yvan Saeysd, Jan Wuytsd, Kamel Jabbarij, Chris Bowlerk, Olivier Panaudi, BenoıˆtPie´ gui, Steven G. Ballk, Jean-Philippe Ralk, Franc¸ois-Yves Bougeta, Gwenael Piganeaua, Bernard De Baetsh, Andre´ Picarda,l, Michel Delsenyi, Jacques Demaillec, Yves Van de Peerd,m, and Herve´ Moreaua,m aObservatoire Oce´anologique, Laboratoire Arago, Unite´Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France; cInstitut de Ge´ne´ tique Humaine, Unite´Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France; dDepartment of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and eLaboratoire Associe´de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, 9052 Ghent, Belgium; fRosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149; gStation Biologique, Unite´Mixte de Recherche 7144, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP74, 29682 Roscoff Cedex, France; hDepartment of Applied Mathematics, Biometrics and -
Comparative Genome Evolution Working Group
Comparative Genome Evolution Working Group COMPARATIVE GENOME EVOLUTION MODIFIED PROPOSAL Introduction Analysis of comparative genomic sequence information from a well-chosen set of organisms is, at present, one of the most effective approaches available to advance biomedical research. The following document describes rationales and plans for selecting targets for genome sequencing that will provide insight into a number of major biological questions that broadly underlie major areas of research funded by the National Institutes of Health, including studies of gene regulation, understanding animal development, and understanding gene and protein function. Genomic sequence data is a fundamental information resource that is required to address important questions about biology: What is the genomic basis for the advent of major morphogenetic or physiological innovations during evolution? How have genomes changed with the addition of new features observed in the eukaryotic lineage, for example the development of an adaptive immune system, an organized nervous system, bilateral symmetry, or multicellularity? What are the genomic correlates or bases for major evolutionary phenomena such as evolutionary rates; speciation; genome reorganization, and origins of variation? Another vital use to which genomic sequence data are applied is the development of more robust information about important non-human model systems used in biomedical research, i.e. how can we identify conserved functional regions in the existing genome sequences of important non- mammalian model systems, so that we can better understand fundamental aspects of, for example, gene regulation, replication, or interactions between genes? NHGRI established a working group to provide the Institute with well-considered scientific thought about the genomic sequences that would most effectively address these questions. -
Atlas of the Flora of New England: Fabaceae
Angelo, R. and D.E. Boufford. 2013. Atlas of the flora of New England: Fabaceae. Phytoneuron 2013-2: 1–15 + map pages 1– 21. Published 9 January 2013. ISSN 2153 733X ATLAS OF THE FLORA OF NEW ENGLAND: FABACEAE RAY ANGELO1 and DAVID E. BOUFFORD2 Harvard University Herbaria 22 Divinity Avenue Cambridge, Massachusetts 02138-2020 [email protected] [email protected] ABSTRACT Dot maps are provided to depict the distribution at the county level of the taxa of Magnoliophyta: Fabaceae growing outside of cultivation in the six New England states of the northeastern United States. The maps treat 172 taxa (species, subspecies, varieties, and hybrids, but not forms) based primarily on specimens in the major herbaria of Maine, New Hampshire, Vermont, Massachusetts, Rhode Island, and Connecticut, with most data derived from the holdings of the New England Botanical Club Herbarium (NEBC). Brief synonymy (to account for names used in standard manuals and floras for the area and on herbarium specimens), habitat, chromosome information, and common names are also provided. KEY WORDS: flora, New England, atlas, distribution, Fabaceae This article is the eleventh in a series (Angelo & Boufford 1996, 1998, 2000, 2007, 2010, 2011a, 2011b, 2012a, 2012b, 2012c) that presents the distributions of the vascular flora of New England in the form of dot distribution maps at the county level (Figure 1). Seven more articles are planned. The atlas is posted on the internet at http://neatlas.org, where it will be updated as new information becomes available. This project encompasses all vascular plants (lycophytes, pteridophytes and spermatophytes) at the rank of species, subspecies, and variety growing independent of cultivation in the six New England states. -
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 -
Section 4. Guidance Document on Horizontal Gene Transfer Between Bacteria
306 - PART 2. DOCUMENTS ON MICRO-ORGANISMS Section 4. Guidance document on horizontal gene transfer between bacteria 1. Introduction Horizontal gene transfer (HGT) 1 refers to the stable transfer of genetic material from one organism to another without reproduction. The significance of horizontal gene transfer was first recognised when evidence was found for ‘infectious heredity’ of multiple antibiotic resistance to pathogens (Watanabe, 1963). The assumed importance of HGT has changed several times (Doolittle et al., 2003) but there is general agreement now that HGT is a major, if not the dominant, force in bacterial evolution. Massive gene exchanges in completely sequenced genomes were discovered by deviant composition, anomalous phylogenetic distribution, great similarity of genes from distantly related species, and incongruent phylogenetic trees (Ochman et al., 2000; Koonin et al., 2001; Jain et al., 2002; Doolittle et al., 2003; Kurland et al., 2003; Philippe and Douady, 2003). There is also much evidence now for HGT by mobile genetic elements (MGEs) being an ongoing process that plays a primary role in the ecological adaptation of prokaryotes. Well documented is the example of the dissemination of antibiotic resistance genes by HGT that allowed bacterial populations to rapidly adapt to a strong selective pressure by agronomically and medically used antibiotics (Tschäpe, 1994; Witte, 1998; Mazel and Davies, 1999). MGEs shape bacterial genomes, promote intra-species variability and distribute genes between distantly related bacterial genera. Horizontal gene transfer (HGT) between bacteria is driven by three major processes: transformation (the uptake of free DNA), transduction (gene transfer mediated by bacteriophages) and conjugation (gene transfer by means of plasmids or conjugative and integrated elements). -
Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes Gabriel A.B
Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes Gabriel A.B. Marais, Bérénice Batut, Vincent Daubin To cite this version: Gabriel A.B. Marais, Bérénice Batut, Vincent Daubin. Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes. Current Biology - CB, Elsevier, 2020, 30 (19), pp.R1083- R1085. 10.1016/j.cub.2020.07.093. hal-03066151 HAL Id: hal-03066151 https://hal.archives-ouvertes.fr/hal-03066151 Submitted on 15 Dec 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. DISPATCH Genome Evolution: Mutation is the Main Driver of Genome Size in Prokaryotes Gabriel A.B. Marais1, Bérénice Batut2, and Vincent Daubin1 1Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F- 69622 Villeurbanne, France 2Albert-Ludwigs-University Freiburg, Department of Computer Science, 79110 Freiburg, Germany Summary Despite intense research on genome architecture since the 2000’s, genome-size evolution in prokaryotes has remained puzzling. Using a phylogenetic approach, a new study found that increased mutation rate is associated with gene loss and reduced genome size in prokaryotes. In 2003 [1] and later in 2007 in his book “The Origins of Genome Architecture” [2], Lynch developed his influential theory that a genome’s complexity, represented by its size, is primarily the result of genetic drift. -
559.Full.Pdf
Copyright 0 1992 by the Genetics Society of America The Structure and Evolutionof Subtelomeric Y‘ Repeats in Saccharomyces cerevisiae Edward J.Louis’ and James E. Haber Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-91 10 Manuscript received September 25, 199 1 Accepted for publication March 28, 1992 ABSTRACT The subtelomeric Y’ family of repeated DNA sequences in the yeast Saccharomyces cerevisiae is of unknown origin and function. Y’s vary in copy number and location among strains. Eight Y‘s, from two strains, were cloned and sequenced over the same 3.2-kb interval in order to assess the within- and between-strain variation as well as address their origin and function. One entireY’ sequence was reconstructed from two clones presented here and apreviously sequenced 833-bp region. It contains two large overlapping open reading frames (ORFs). The putative protein sequences have no strong homologies to any known proteins except for one region that has 27% identity with RNA helicases. RNA homologous to each ORF was detected. Comparison of the sequences revealed that the known long (Y’-L) and short (Y’-S) size classes, which coexist within cells, differ by several insertions and/or deletions within this region. The Y’-Ls from strain Y55 alsodiffer from those of strain YPl by several short deletions in the same region. Most of these deletions appear to have occurred between short (2-10 bp) direct repeats. The single base pair polymorphisms and the deletions are clustered in the first half of the interval compared. There is 0.30-1.13% divergence among Y’-Ls within a strain and 1.15-1.75% divergence between strains in the interval. -
Evolution of Genome Size
Evolution of Genome Advanced article Article Contents Size • Introduction • How Much Variation Is There? Stephen I Wright, Department of Ecology and Evolutionary Biology, University • What Types of DNA Drive Genome Size of Toronto, Toronto, Ontario, Canada Variation? • Neutral Model • Nearly Neutral Model • Adaptive Hypotheses • Transposable Element Evolution • Conclusion • Acknowledgements Online posting date: 16th January 2017 The size of the genome represents one of the most in the last century. While considerable progress has been made strikingly variable yet poorly understood traits in the characterisation of the extent of genome size variation, in eukaryotic organisms. Genomic comparisons the dominant evolutionary processes driving genome size evolu- suggest that most properties of genomes tend tion remain subject to considerable debate. Large-scale genome sequencing is enabling new insights into both the proximate to increase with genome size, but the fraction causes and evolutionary forces governing genome size differ- of the genome that comprises transposable ele- ences. ments (TEs) and other repetitive elements tends to increase disproportionately. Neutral, nearly neutral and adaptive models for the evolution of How Much Variation Is There? genome size have been proposed, but strong evi- dence for the general importance of any of these Because determining the amount of DNA (deoxyribonucleic models remains lacking, and improved under- acid) in a cell has been much more straightforward and cheaper standing of factors driving the -
Repeat Sequence Turnover Shifts Fundamentally in Species with Large Genomes
Novak et al. Repeat sequence turnover shifts fundamentally in species with large genomes Repeat sequence turnover shifts fundamentally in species with large genomes Petr Novák1, Maïté S. Guignard2,3, Pavel Neumann1, Laura J. Kelly2,3, Jelena Mlinarec4, Andrea Koblížková1, Steven Dodsworth3,5, Aleš Kovařík6, Jaume Pellicer2, Wencai Wang3,8, Jiří Macas1*, Ilia J. Leitch2*, Andrew R. Leitch3* 1 Biology Centre, Czech Academy of Sciences, České Budějovice, CZ-37005, Czech Republic 2 Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK 3 School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK 4 Division of Molecular Biology, Department of Biology, University of Zagreb, Croatia 5 School of Life Sciences, University of Bedfordshire, Luton LU1 3JU, UK 6 Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic 7 Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain 8 Guangzhou University of Chinese Medicine, Guangzhou, 510405, China *Authors for Correspondence: Ilia J Leitch, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK. Telephone: +44 208 332 5329. Email: [email protected] Jiří Macas, Biology Centre, Czech Academy of Sciences, České Budějovice, CZ-37005, Czech Republic. Telephone: + 420 38 777 5516. Email: [email protected] Andrew R Leitch, School of Biological and Chemical Sciences, Queen Mary University of London. London E1 4NS. Telephone: +44 207 882 5294. Email: [email protected] Petr Novák, [email protected] Ilia J. Leitch, [email protected] Jelena Mlinarec, [email protected] Laura Kelly, [email protected] Andrea Koblížková, [email protected] Pavel Neumann, [email protected] Steven Dodsworth, [email protected] Maïté Guignard, [email protected] Wencai Wang, [email protected] Aleš Kovřík, [email protected] Jaume Pellicer, [email protected] Jiří Macas, [email protected] Andrew R. -
Best Practices for Whole Genome Sequencing Using the Sequel System
Best Practices for Whole Genome Sequencing Using the Sequel System Justin Blethrow, Nick Sisneros, Shreyasee Chakraborty, Sarah Kingan, Richard Hall, Joan Wilson, Christine Lambert, Kevin Eng, Emily Hatas and Primo Baybayan PacBio, 1305 O’Brien Dr., Menlo Park, CA 94025 Library Construction Abstract Recommendations Data Analysis Plant and animal whole genome sequencing has proven to Recommended Shearing Devices for Large-insert Fragments Hierarchical Genome Assembly Process (HGAP) and Polishing be challenging, particularly due to genome size, high For shearing DNA, PacBio recommends either: 1) needle shearing with a 26 G needle, which density of repetitive elements and heterozygosity. The allows for flexibility in number of shearing pulses with the needle or 2) the Megaruptor, a simple, Sequel System delivers long reads, high consensus automated, and highly reproducible system to fragment DNA up to 75 kb. accuracy and uniform coverage, enabling more complete, accurate, and contiguous assemblies of these large complex genomes. The latest Sequel chemistry increases yield up to 8 Gb per SMRT Cell for long insert libraries >20 kb and up to 10 Gb per SMRT Cell for libraries >40 kb. In addition, the recently released SMRTbell Express Megaruptor® DNA Shearing System Template Prep Kit reduces the time (~3 hours) and DNA Demonstration of Needle Shearing input (~3 µg), making the workflow easy to use for multi- SMRT Cell projects. 1 2 3 4 5 Here, we recommend the best practices for whole genome HGAP1 utilizes all PacBio data using the longest reads for contiguity and all reads to sequencing and de novo assembly of complex plant and generate high-quality de novo assemblies with high consensus accuracy (>QV50). -
Kinetic Parameters of Trans Scission by Extended HDV-Like Ribozymes and the Prospect for the Discovery of Genomic Trans-Cleaving Rnas
UC Irvine UC Irvine Previously Published Works Title Kinetic Parameters of trans Scission by Extended HDV-like Ribozymes and the Prospect for the Discovery of Genomic trans-Cleaving RNAs. Permalink https://escholarship.org/uc/item/1894s91p Journal Biochemistry, 57(9) ISSN 0006-2960 Authors Webb, Chiu-Ho T Lupták, Andrej Publication Date 2018-03-01 DOI 10.1021/acs.biochem.7b00789 Supplemental Material https://escholarship.org/uc/item/1894s91p#supplemental Peer reviewed eScholarship.org Powered by the California Digital Library University of California Article Cite This: Biochemistry 2018, 57, 1440−1450 pubs.acs.org/biochemistry Kinetic Parameters of trans Scission by Extended HDV-like Ribozymes and the Prospect for the Discovery of Genomic trans- Cleaving RNAs Chiu-Ho T. Webb†,∥ and Andrej Luptaḱ*,†,‡,§ † Department of Molecular Biology and Biochemistry, University of CaliforniaIrvine, Irvine, California 92697, United States ‡ Department of Pharmaceutical Sciences, University of CaliforniaIrvine, Irvine, California 92697, United States § Department of Chemistry, University of CaliforniaIrvine, Irvine, California 92697, United States *S Supporting Information ABSTRACT: Hepatitis delta virus (HDV)-like ribozymes are self- cleaving catalytic RNAs with a widespread distribution in nature and biological roles ranging from self-scission during rolling-circle replication in viroids to co-transcriptional processing of eukaryotic retrotransposons, among others. The ribozymes fold into a double pseudoknot with a common catalytic core motif and highly variable peripheral domains. Like other self-cleaving ribozymes, HDV-like ribozymes can be converted into trans-acting catalytic RNAs by bisecting the self-cleaving variants at non- essential loops. Here we explore the trans-cleaving activity of ribozymes derived from the largest examples of the ribozymes (drz-Agam-2 family), which contain an extended domain between the substrate strand and the rest of the RNA.