Search: onr:"swepub:oai:DiVA.org:uu-350545" >
The Physcomitrella ...
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
-
- Lang, Daniel (author)
- Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.
-
- Ullrich, Kristian K. (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Max Planck Inst Evolutionary Biol, August Thienemann Str 2, D-24306 Plon, Germany.
-
- Murat, Florent (author)
- INRA, UMR Genet Divers & Ecophysiol Cereals GDEC 1095, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France.
-
show more...
-
- Fuchs, Joerg (author)
- Leibniz Inst Plant Genet & Crop Plant Res IPK, Corrensstr 3, D-06466 Ot Gatersleben, Stadt Seeland, Germany.
-
- Jenkins, Jerry (author)
- HudsonAlpha Inst Biotechnol, Huntsville, AL USA.
-
- Haas, Fabian B. (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.
-
- Piednoel, Mathieu (author)
- Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, Carl von Linne Weg 10, D-50829 Cologne, Germany.
-
- Gundlach, Heidrun (author)
- Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.
-
- Van Bel, Michiel (author)
- VIB Ctr Plant Syst Biol, Technol Pk 927, B-9052 Ghent, Belgium.;Univ Ghent, Dept Plant Biotechnol & Bioinformat, Technol Pk 927, B-9052 Ghent, Belgium.
-
- Meyberg, Rabea (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.
-
- Vives, Cristina (author)
- UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain.
-
- Morata, Jordi (author)
- UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain.
-
- Symeonidi, Aikaterini (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Inst Res Biomed IRB Barcelona, Barcelona, Spain.
-
- Hiss, Manuel (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.
-
- Muchero, Wellington (author)
- Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.
-
- Kamisugi, Yasuko (author)
- Univ Leeds, Fac Biol Sci, Ctr Plant Sci, Leeds LS2 9JT, W Yorkshire, England.
-
- Saleh, Omar (author)
- Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Humboldt Univ, Plant Mol Cell Biol, D-10115 Berlin, Germany.
-
- Blanc, Guillaume (author)
- Aix Marseille Univ, Struct & Genom Informat Lab IGS, IMM FR 3479, CNRS,UMR 7256, Marseille, France.
-
- Decker, Eva L. (author)
- Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.
-
- van Gessel, Nico (author)
- Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.
-
- Grimwood, Jane (author)
- HudsonAlpha Inst Biotechnol, Huntsville, AL USA.;US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.
-
- Hayes, Richard D. (author)
- US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.
-
- Graham, Sean W. (author)
- Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
-
- Gunter, Lee E. (author)
- Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.
-
- McDaniel, Stuart F. (author)
- Univ Florida, Dept Biol, Gainesville, FL 32611 USA.
-
- Hoernstein, Sebastian N. W. (author)
- Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.
-
- Larsson, Anders (author)
- Uppsala universitet,Systematisk biologi
-
- Li, Fay-Wei (author)
- Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA.
-
- Perroud, Pierre-Francois (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.
-
- Phillips, Jeremy (author)
- US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.
-
- Ranjan, Priya (author)
- Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.
-
- Rokshar, Daniel S. (author)
- US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.;Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA.
-
- Rothfels, Carl J. (author)
- Univ Calif Berkeley, Univ Herbarium, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA.
-
- Schneider, Lucas (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Goethe Univ Frankfurt, Inst Transfus Med & Immunohematol, Sandhofstr 1, D-60528 Frankfurt, Germany.;German Red Cross Blood Serv, Sandhofstr 1, D-60528 Frankfurt, Germany.
-
- Shu, Shengqiang (author)
- US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.
-
- Stevenson, Dennis W. (author)
- New York Bot Garden, Bronx, NY 10458 USA.
-
- Thummler, Fritz (author)
- Vertis Biotechnol AG, Lise Meitner Str 30, D-85354 Freising Weihenstephan, Germany.
-
- Tillich, Michael (author)
- Max Planck Inst Mol Plant Physiol, Muehlenberg 1, D-14476 Potsdam, Germany.
-
- Aguilar, Juan C. Villarreal (author)
- Univ Laval, Dept Biol, Quebec City, PQ G1V 0A6, Canada.
-
- Widiez, Thomas (author)
- Univ Geneva, Dept Plant Biol, Sci 3, CH-1211 Geneva 4, Switzerland.;Rutgers State Univ, Dept Plant Biol & Pathol, New Brunswick, NJ 08901 USA.;UCB Lyon 1, Lab Reprod & Dev Plantes, Univ Lyon, ENS Lyon,CNRS,INRA, F-69342 Lyon, France.
-
- Wong, Gane Ka-Shu (author)
- Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada.;Univ Alberta, Dept Med, Edmonton, AB T6G 2E1, Canada.;BGI Shenzhen, Shenzhen 518083, Peoples R China.
-
- Wymore, Ann (author)
- Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.
-
- Zhang, Yong (author)
- Shenzhen Huahan Gene Life Technol Co Ltd, Shenzhen, Peoples R China.
-
- Zimmer, Andreas D. (author)
- Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Univ Freiburg, Fac Med, Inst Human Genet, Med Ctr, Freiburg, Germany.
-
- Quatrano, Ralph S. (author)
- Washington Univ, Dept Biol, Campus Box 1137, St Louis, MO 63130 USA.
-
- Mayer, Klaus F. X. (author)
- Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.;Tech Univ Munich, WZW, Munich, Germany.
-
- Goodstein, David (author)
- US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.
-
- Casacuberta, Josep M. (author)
- UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain.
-
- Vandepoele, Klaas (author)
- VIB Ctr Plant Syst Biol, Technol Pk 927, B-9052 Ghent, Belgium.;Univ Ghent, Dept Plant Biotechnol & Bioinformat, Technol Pk 927, B-9052 Ghent, Belgium.
-
- Reski, Ralf (author)
- Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, Schaenzlestr 18, D-79104 Freiburg, Germany.
-
- Cuming, Andrew C. (author)
- Univ Leeds, Fac Biol Sci, Ctr Plant Sci, Leeds LS2 9JT, W Yorkshire, England.
-
- Tuskan, Gerald A. (author)
- Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.
-
- Maumus, Florian (author)
- Univ Paris Saclay, INRA, URGI, F-78026 Versailles, France.
-
- Salse, Jerome (author)
- INRA, UMR Genet Divers & Ecophysiol Cereals GDEC 1095, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France.
-
- Schmutz, Jeremy (author)
- HudsonAlpha Inst Biotechnol, Huntsville, AL USA.;US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.
-
- Rensing, Stefan A. (author)
- Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, Schaenzlestr 18, D-79104 Freiburg, Germany.
-
show less...
-
Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany;Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany. Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Max Planck Inst Evolutionary Biol, August Thienemann Str 2, D-24306 Plon, Germany. (creator_code:org_t)
- 2018-01-19
- 2018
- English.
-
In: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 93:3, s. 515-533
- Related links:
-
https://onlinelibrar...
-
show more...
-
https://urn.kb.se/re...
-
https://doi.org/10.1...
-
show less...
Abstract
Subject headings
Close
- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Keyword
- evolution
- genome
- chromosome
- plant
- moss
- methylation
- duplication
- synteny
- Physcomitrella patens
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
-
Lang, Daniel
-
Ullrich, Kristia ...
-
Murat, Florent
-
Fuchs, Joerg
-
Jenkins, Jerry
-
Haas, Fabian B.
-
show more...
-
Piednoel, Mathie ...
-
Gundlach, Heidru ...
-
Van Bel, Michiel
-
Meyberg, Rabea
-
Vives, Cristina
-
Morata, Jordi
-
Symeonidi, Aikat ...
-
Hiss, Manuel
-
Muchero, Welling ...
-
Kamisugi, Yasuko
-
Saleh, Omar
-
Blanc, Guillaume
-
Decker, Eva L.
-
van Gessel, Nico
-
Grimwood, Jane
-
Hayes, Richard D ...
-
Graham, Sean W.
-
Gunter, Lee E.
-
McDaniel, Stuart ...
-
Hoernstein, Seba ...
-
Larsson, Anders
-
Li, Fay-Wei
-
Perroud, Pierre- ...
-
Phillips, Jeremy
-
Ranjan, Priya
-
Rokshar, Daniel ...
-
Rothfels, Carl J ...
-
Schneider, Lucas
-
Shu, Shengqiang
-
Stevenson, Denni ...
-
Thummler, Fritz
-
Tillich, Michael
-
Aguilar, Juan C. ...
-
Widiez, Thomas
-
Wong, Gane Ka-Sh ...
-
Wymore, Ann
-
Zhang, Yong
-
Zimmer, Andreas ...
-
Quatrano, Ralph ...
-
Mayer, Klaus F. ...
-
Goodstein, David
-
Casacuberta, Jos ...
-
Vandepoele, Klaa ...
-
Reski, Ralf
-
Cuming, Andrew C ...
-
Tuskan, Gerald A ...
-
Maumus, Florian
-
Salse, Jerome
-
Schmutz, Jeremy
-
Rensing, Stefan ...
-
show less...
- About the subject
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Bioinformatics a ...
- Articles in the publication
-
The Plant Journa ...
- By the university
-
Uppsala University