Authors: Daniel Lang, Kristian K. Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, Fabian B. Haas, Mathieu Piednoel, Heidrun Gundlach, Michiel Van Bel, Rabea Meyberg, Cristina Vives, Jordi Morata, Aikaterini Symeonidi, Manuel Hiss, Wellington Muchero, Yasuko Kamisugi, Omar Saleh, Guillaume Blanc, Eva L. Decker, Nico van Gessel, Jane Grimwood, Richard D. Hayes, Sean W. Graham, Lee E. Gunter, Stuart F. McDaniel, Sebastian N.W. Hoernstein, Anders Larsson, Fay‐Wei Li, Pierre‐François Perroud, Jeremy Phillips, Priya Ranjan, Daniel S. Rokshar, Carl J. Rothfels, Lucas Schneider, Shengqiang Shu, Dennis W. Stevenson, Fritz Thümmler, Michael Tillich, Juan C. Villarreal Aguilar, Thomas Widiez, Gane Ka‐Shu Wong, Ann Wymore, Yong Zhang, Andreas D. Zimmer, Ralph S. Quatrano, Klaus F.X. Mayer, David Goodstein, Josep M. Casacuberta, Klaas Vandepoele, Ralf Reski, Andrew C. Cuming, Gerald A. Tuskan, Florian Maumus, Jérome Salse, Jeremy Schmutz, Stefan A. Rensing

Institutions:

  • Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
  • Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
  • INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100 Clermont‐Ferrand, France
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D‐06466 Stadt Seeland, Germany
  • HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
  • Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl‐von‐Linné Weg 10, D‐50829 Cologne, Germany
  • VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
  • Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B‐9052 Gent, Belgium
  • Center for Research in Agricultural Genomics, CRAG (CSIC‐IRTA‐UAB‐UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain
  • Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 USA
  • Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT UK
  • Structural and Genomic Information Laboratory (IGS), Aix‐Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
  • Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
  • DOE Joint Genome Institute, Walnut Creek, CA, 94598 USA
  • Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
  • Department of Biology, University of Florida, Gainesville, FL, 32611 USA
  • Vertis Biotechnologie AG, Lise‐Meitner‐Str. 30, 85354 Freising, Germany
  • Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam‐Golm, Germany
  • Department of Biology, Université Laval, Québec, G1V 0A6 Canada
  • Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH‐1211 Switzerland
  • Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901 USA
  • Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9 Canada
  • Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1 Canada
  • BGI‐Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083 China
  • Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
  • Department of Biology, Washington University, St. Louis, MO, USA
  • URGI, INRA, Université Paris‐Saclay, 78026 Versailles, France

Acknowledgements: Riccardo Aiese Cigliano and Walter Sanseverino

Publication: The Plant Journal

Date: December, 2017

Full paper: The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution

Abstract:

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome‐scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene‐ and TE‐rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono‐centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein‐coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure‐based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant‐specific cell growth and tissue organization. The P. patens genome lacks the TE‐rich pericentromeric and gene‐rich distal regions typical for most flowering plant genomes. More non‐seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.