The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

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Fältnamn	Indikatorer	Metadata
000		10854naa a2201081 4500
001		oai:DiVA.org:uu-350545
003		SwePub
008		180521s2018 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3505452 URI
024	7	a https://doi.org/10.1111/tpj.138012 DOI
040		a (SwePub)uu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Lang, Danielu Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.4 aut
245	1 0	a The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
264		c 2018-01-19
264	1	b Wiley,c 2018
338		a print2 rdacarrier
500		a De två första författarna delar förstaförfattarskapet.
520		a 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.
650	7	a NATURVETENSKAPx Biologix Bioinformatik och systembiologi0 (SwePub)106102 hsv//swe
650	7	a NATURAL SCIENCESx Biological Sciencesx Bioinformatics and Systems Biology0 (SwePub)106102 hsv//eng
653		a evolution
653		a genome
653		a chromosome
653		a plant
653		a moss
653		a methylation
653		a duplication
653		a synteny
653		a Physcomitrella patens
700	1	a Ullrich, Kristian K.u Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Max Planck Inst Evolutionary Biol, August Thienemann Str 2, D-24306 Plon, Germany.4 aut
700	1	a Murat, Florentu INRA, UMR Genet Divers & Ecophysiol Cereals GDEC 1095, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France.4 aut
700	1	a Fuchs, Joergu Leibniz Inst Plant Genet & Crop Plant Res IPK, Corrensstr 3, D-06466 Ot Gatersleben, Stadt Seeland, Germany.4 aut
700	1	a Jenkins, Jerryu HudsonAlpha Inst Biotechnol, Huntsville, AL USA.4 aut
700	1	a Haas, Fabian B.u Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.4 aut
700	1	a Piednoel, Mathieuu Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, Carl von Linne Weg 10, D-50829 Cologne, Germany.4 aut
700	1	a Gundlach, Heidrunu Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.4 aut
700	1	a Van Bel, Michielu 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.4 aut
700	1	a Meyberg, Rabeau Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.4 aut
700	1	a Vives, Cristinau UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain.4 aut
700	1	a Morata, Jordiu UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain.4 aut
700	1	a Symeonidi, Aikateriniu Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Inst Res Biomed IRB Barcelona, Barcelona, Spain.4 aut
700	1	a Hiss, Manuelu Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.4 aut
700	1	a Muchero, Wellingtonu Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.4 aut
700	1	a Kamisugi, Yasukou Univ Leeds, Fac Biol Sci, Ctr Plant Sci, Leeds LS2 9JT, W Yorkshire, England.4 aut
700	1	a Saleh, Omaru Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Humboldt Univ, Plant Mol Cell Biol, D-10115 Berlin, Germany.4 aut
700	1	a Blanc, Guillaumeu Aix Marseille Univ, Struct & Genom Informat Lab IGS, IMM FR 3479, CNRS,UMR 7256, Marseille, France.4 aut
700	1	a Decker, Eva L.u Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.4 aut
700	1	a van Gessel, Nicou Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.4 aut
700	1	a Grimwood, Janeu HudsonAlpha Inst Biotechnol, Huntsville, AL USA.;US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.4 aut
700	1	a Hayes, Richard D.u US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.4 aut
700	1	a Graham, Sean W.u Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.4 aut
700	1	a Gunter, Lee E.u Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.4 aut
700	1	a McDaniel, Stuart F.u Univ Florida, Dept Biol, Gainesville, FL 32611 USA.4 aut
700	1	a Hoernstein, Sebastian N. W.u Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.4 aut
700	1	a Larsson, Andersu Uppsala universitet,Systematisk biologi4 aut0 (Swepub:uu)andla958
700	1	a Li, Fay-Weiu Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA.4 aut
700	1	a Perroud, Pierre-Francoisu Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.4 aut
700	1	a Phillips, Jeremyu US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.4 aut
700	1	a Ranjan, Priyau Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.4 aut
700	1	a Rokshar, Daniel S.u US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.;Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA.4 aut
700	1	a Rothfels, Carl J.u Univ Calif Berkeley, Univ Herbarium, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA.4 aut
700	1	a Schneider, Lucasu 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.4 aut
700	1	a Shu, Shengqiangu US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.4 aut
700	1	a Stevenson, Dennis W.u New York Bot Garden, Bronx, NY 10458 USA.4 aut
700	1	a Thummler, Fritzu Vertis Biotechnol AG, Lise Meitner Str 30, D-85354 Freising Weihenstephan, Germany.4 aut
700	1	a Tillich, Michaelu Max Planck Inst Mol Plant Physiol, Muehlenberg 1, D-14476 Potsdam, Germany.4 aut
700	1	a Aguilar, Juan C. Villarrealu Univ Laval, Dept Biol, Quebec City, PQ G1V 0A6, Canada.4 aut
700	1	a Widiez, Thomasu 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.4 aut
700	1	a Wong, Gane Ka-Shuu 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.4 aut
700	1	a Wymore, Annu Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.4 aut
700	1	a Zhang, Yongu Shenzhen Huahan Gene Life Technol Co Ltd, Shenzhen, Peoples R China.4 aut
700	1	a Zimmer, Andreas D.u Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Univ Freiburg, Fac Med, Inst Human Genet, Med Ctr, Freiburg, Germany.4 aut
700	1	a Quatrano, Ralph S.u Washington Univ, Dept Biol, Campus Box 1137, St Louis, MO 63130 USA.4 aut
700	1	a Mayer, Klaus F. X.u Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.;Tech Univ Munich, WZW, Munich, Germany.4 aut
700	1	a Goodstein, Davidu US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.4 aut
700	1	a Casacuberta, Josep M.u UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain.4 aut
700	1	a Vandepoele, Klaasu 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.4 aut
700	1	a Reski, Ralfu 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.4 aut
700	1	a Cuming, Andrew C.u Univ Leeds, Fac Biol Sci, Ctr Plant Sci, Leeds LS2 9JT, W Yorkshire, England.4 aut
700	1	a Tuskan, Gerald A.u Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA.4 aut
700	1	a Maumus, Florianu Univ Paris Saclay, INRA, URGI, F-78026 Versailles, France.4 aut
700	1	a Salse, Jeromeu INRA, UMR Genet Divers & Ecophysiol Cereals GDEC 1095, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France.4 aut
700	1	a Schmutz, Jeremyu HudsonAlpha Inst Biotechnol, Huntsville, AL USA.;US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.4 aut
700	1	a Rensing, Stefan A.u Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, Schaenzlestr 18, D-79104 Freiburg, Germany.4 aut
710	2	a Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.b Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Max Planck Inst Evolutionary Biol, August Thienemann Str 2, D-24306 Plon, Germany.4 org
773	0	t The Plant Journald : Wileyg 93:3, s. 515-533q 93:3<515-533x 0960-7412x 1365-313X
856	4	u https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tpj.13801
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-350545
856	4 8	u https://doi.org/10.1111/tpj.13801

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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...

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By the university: Uppsala University

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