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

Abstract

Here, 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–richmore » 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.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3];  [4];  [5]; ORCiD logo [2];  [6];  [7];  [8];  [2];  [9];  [9];  [2];  [2];  [10]; ORCiD logo [11];  [12];  [13];  [12];  [12] more »;  [14];  [15];  [16];  [10];  [17];  [12];  [18];  [19]; ORCiD logo [2];  [15];  [10];  [20];  [21];  [2];  [15];  [22];  [23];  [24];  [25];  [26];  [27];  [10];  [28];  [12];  [29];  [30];  [15];  [9]; ORCiD logo [8]; ORCiD logo [12]; ORCiD logo [11];  [10];  [31];  [32];  [14]; ORCiD logo [33] « less
  1. Univ. of Freiburg, Freiburg (Germany); Helmholtz Center Munich, Neuherberg (Germany)
  2. Univ. of Marburg, Marburg (Germany)
  3. UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), Clermont-Ferrand (France)
  4. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland (Germany)
  5. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  6. Max Planck Institute for Plant Breeding Research, Cologne (Germany)
  7. Helmholtz Center Munich, Neuherberg (Germany)
  8. VIB Center for Plant Systems Biology, Ghent (Belgium); Ghent Univ., Ghent (Belgium)
  9. Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona (Spain)
  10. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  11. Univ. of Leeds, Leeds (United Kingdom)
  12. Univ. of Freiburg, Freiburg (Germany)
  13. Aix-Marseille Univ., Marseille (France)
  14. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  15. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  16. Univ. of British Columbia, Vancouver, BC (Canada)
  17. Univ. of Florida, Gainesville, FL (United States)
  18. Uppsala Univ., Uppsala (Sweden)
  19. Boyce Thompson Institute, Ithaca, NY (United States)
  20. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
  21. Univ. of California, Berkeley, CA (United States)
  22. New York Botanical Garden, Bronx, NY (United States)
  23. Vertis Biotechnologie AG, Freising (Germany)
  24. Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm (Germany)
  25. Univ. Laval, QC (Canada)
  26. Univ. of Geneva, Geneva (Switzerland); Rutgers Univ., New Brunswick, NJ (United States)
  27. Univ. of AlbertaEdmonton, AB (Canada); BGI-Shenzhen, Yantian District Shenzhen (China)
  28. Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen (China)
  29. Washington Univ., St. Louis, MO (United States)
  30. Helmholtz Center Munich, Neuherberg (Germany); WZW, Technical Univ. Munich, Munich (Germany)
  31. Univ. Paris-Saclay, Versailles (France)
  32. INRA, Clermont-Ferrand (France)
  33. Univ. of Marburg, Marburg (Germany); Univ. of Freiburg, Freiburg (Germany)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1439140
Alternate Identifier(s):
OSTI ID: 1456995
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 93; Journal Issue: 3; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; evolution; genome; chromosome; plant; moss; methylation; duplication; synteny; Physcomitrella patens

Citation Formats

Lang, Daniel, Ullrich, Kristian K., Murat, Florent, Fuchs, Jorg, Jenkins, Jerry, Haas, Fabian B., Piednoel, Mathieu, Gundlach, Heidrun, Van Bel, Michiel, Meyberg, Rabea, Vives, Cristina, Morata, Jordi, Symeonidi, Aikaterini, Hiss, Manuel, Muchero, Wellington, 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 F., Hoernstein, Sebastian N. W., Larsson, Anders, Li, Fay -Wei, Perroud, Pierre -Francois, Phillips, Jeremy, Ranjan, Priya, Rokshar, Daniel S., Rothfels, Carl J., Schneider, Lucas, Shu, Shengqiang, Stevenson, Dennis W., Thummler, Fritz, Tillich, Michael, Villarreal Aguilar, Juan C., Widiez, Thomas, Wong, Gane Ka-Shu, Wymore, Ann, Zhang, Yong, Zimmer, Andreas D., Quatrano, Ralph S., Mayer, Klaus F. X., Goodstein, David, Casacuberta, Josep M., Vandepoele, Klaas, Reski, Ralf, Cuming, Andrew C., Tuskan, Gerald A., Maumus, Florian, Salse, Jerome, Schmutz, Jeremy, and Rensing, Stefan A. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. United States: N. p., 2017. Web. doi:10.1111/tpj.13801.
Lang, Daniel, Ullrich, Kristian K., Murat, Florent, Fuchs, Jorg, Jenkins, Jerry, Haas, Fabian B., Piednoel, Mathieu, Gundlach, Heidrun, Van Bel, Michiel, Meyberg, Rabea, Vives, Cristina, Morata, Jordi, Symeonidi, Aikaterini, Hiss, Manuel, Muchero, Wellington, 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 F., Hoernstein, Sebastian N. W., Larsson, Anders, Li, Fay -Wei, Perroud, Pierre -Francois, Phillips, Jeremy, Ranjan, Priya, Rokshar, Daniel S., Rothfels, Carl J., Schneider, Lucas, Shu, Shengqiang, Stevenson, Dennis W., Thummler, Fritz, Tillich, Michael, Villarreal Aguilar, Juan C., Widiez, Thomas, Wong, Gane Ka-Shu, Wymore, Ann, Zhang, Yong, Zimmer, Andreas D., Quatrano, Ralph S., Mayer, Klaus F. X., Goodstein, David, Casacuberta, Josep M., Vandepoele, Klaas, Reski, Ralf, Cuming, Andrew C., Tuskan, Gerald A., Maumus, Florian, Salse, Jerome, Schmutz, Jeremy, & Rensing, Stefan A. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. United States. doi:10.1111/tpj.13801.
Lang, Daniel, Ullrich, Kristian K., Murat, Florent, Fuchs, Jorg, Jenkins, Jerry, Haas, Fabian B., Piednoel, Mathieu, Gundlach, Heidrun, Van Bel, Michiel, Meyberg, Rabea, Vives, Cristina, Morata, Jordi, Symeonidi, Aikaterini, Hiss, Manuel, Muchero, Wellington, 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 F., Hoernstein, Sebastian N. W., Larsson, Anders, Li, Fay -Wei, Perroud, Pierre -Francois, Phillips, Jeremy, Ranjan, Priya, Rokshar, Daniel S., Rothfels, Carl J., Schneider, Lucas, Shu, Shengqiang, Stevenson, Dennis W., Thummler, Fritz, Tillich, Michael, Villarreal Aguilar, Juan C., Widiez, Thomas, Wong, Gane Ka-Shu, Wymore, Ann, Zhang, Yong, Zimmer, Andreas D., Quatrano, Ralph S., Mayer, Klaus F. X., Goodstein, David, Casacuberta, Josep M., Vandepoele, Klaas, Reski, Ralf, Cuming, Andrew C., Tuskan, Gerald A., Maumus, Florian, Salse, Jerome, Schmutz, Jeremy, and Rensing, Stefan A. Wed . "The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution". United States. doi:10.1111/tpj.13801. https://www.osti.gov/servlets/purl/1439140.
@article{osti_1439140,
title = {The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution},
author = {Lang, Daniel and Ullrich, Kristian K. and Murat, Florent and Fuchs, Jorg and Jenkins, Jerry and Haas, Fabian B. and Piednoel, Mathieu and Gundlach, Heidrun and Van Bel, Michiel and Meyberg, Rabea and Vives, Cristina and Morata, Jordi and Symeonidi, Aikaterini and Hiss, Manuel and Muchero, Wellington and Kamisugi, Yasuko and Saleh, Omar and Blanc, Guillaume and Decker, Eva L. and van Gessel, Nico and Grimwood, Jane and Hayes, Richard D. and Graham, Sean W. and Gunter, Lee E. and McDaniel, Stuart F. and Hoernstein, Sebastian N. W. and Larsson, Anders and Li, Fay -Wei and Perroud, Pierre -Francois and Phillips, Jeremy and Ranjan, Priya and Rokshar, Daniel S. and Rothfels, Carl J. and Schneider, Lucas and Shu, Shengqiang and Stevenson, Dennis W. and Thummler, Fritz and Tillich, Michael and Villarreal Aguilar, Juan C. and Widiez, Thomas and Wong, Gane Ka-Shu and Wymore, Ann and Zhang, Yong and Zimmer, Andreas D. and Quatrano, Ralph S. and Mayer, Klaus F. X. and Goodstein, David and Casacuberta, Josep M. and Vandepoele, Klaas and Reski, Ralf and Cuming, Andrew C. and Tuskan, Gerald A. and Maumus, Florian and Salse, Jerome and Schmutz, Jeremy and Rensing, Stefan A.},
abstractNote = {Here, 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.},
doi = {10.1111/tpj.13801},
journal = {The Plant Journal},
number = 3,
volume = 93,
place = {United States},
year = {2017},
month = {12}
}

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Cited by: 32 works
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Figures / Tables:

Figure 1. The P. patens life cycle. Figure 1. The P. patens life cycle.: Germination of haploid spores yields the juvenile gametophytic generation, the protonema. Protonema grows two-dimensional by apical (tip) growth and side branching. Protonemata consist of chloroplast-rich chloronema cells, and longer, thinner caulonema cells featuring less chloroplasts and oblique cross walls. Three-faced buds featuring singlemore » apical stem cells emerge from side branches (Harrison et al., 2009) to form the adult gametophytic phase, the leafy gametophores. Gametophores comprise basal, multicellular rhizoids for nutrient supply, as well as non-vascular leaves (phyllids). Gametangia (female archegonia and male antheridia) develop on the gametophores. Upon fertilization of the egg cell by motile spermatozoids the diploid zygote forms and subsequently performs embryogenesis. Spore mother cells in the diploid sporophyte undergo meiosis to form spores.« less

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Works referenced in this record:

DICER-LIKE3 Activity in Physcomitrella patens DICER-LIKE4 Mutants Causes Severe Developmental Dysfunction and Sterility
journal, November 2012

  • Arif, M. Asif; Fattash, Isam; Ma, Zhaorong
  • Molecular Plant, Vol. 5, Issue 6
  • DOI: 10.1093/mp/sss036

EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences
journal, July 2003


De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome
journal, June 2014

  • Szövényi, Péter; Perroud, Pierre-François; Symeonidi, Aikaterini
  • Molecular Ecology Resources, Vol. 15, Issue 1
  • DOI: 10.1111/1755-0998.12284

Model-based Analysis of ChIP-Seq (MACS)
journal, January 2008


BLAT---The BLAST-Like Alignment Tool
journal, March 2002


KNOX2 Genes Regulate the Haploid-to-Diploid Morphological Transition in Land Plants
journal, February 2013


Plant chromosomes from end to end: telomeres, heterochromatin and centromeres
journal, April 2007


i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles
journal, October 2007


Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes
journal, September 2012


Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens : introducing the ecotype Reute
journal, March 2017

  • Hiss, Manuel; Meyberg, Rabea; Westermann, Jens
  • The Plant Journal, Vol. 90, Issue 3
  • DOI: 10.1111/tpj.13501

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years
journal, August 2008

  • Barker, M. S.; Kane, N. C.; Matvienko, M.
  • Molecular Biology and Evolution, Vol. 25, Issue 11
  • DOI: 10.1093/molbev/msn187

Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum
journal, May 2015

  • Vanneste, Kevin; Sterck, Lieven; Myburg, Alexander Andrew
  • The Plant Cell, Vol. 27, Issue 6
  • DOI: 10.1105/tpc.15.00157

Circos: An information aesthetic for comparative genomics
journal, June 2009


TopHat: discovering splice junctions with RNA-Seq
journal, March 2009


A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants
journal, February 2016

  • Ortiz-Ramírez, Carlos; Hernandez-Coronado, Marcela; Thamm, Anna
  • Molecular Plant, Vol. 9, Issue 2
  • DOI: 10.1016/j.molp.2015.12.002

Combined Evidence Annotation of Transposable Elements in Genome Sequences
journal, January 2005


Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


Genome size increases in recently diverged hornwort clades
journal, August 2013


Considering Transposable Element Diversification in De Novo Annotation Approaches
journal, January 2011


Gene duplication as a driver of plant morphogenetic evolution
journal, February 2014


Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana
journal, March 2012

  • Stroud, H.; Otero, S.; Desvoyes, B.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 14
  • DOI: 10.1073/pnas.1203145109

Genome analysis of the moss Physcomitrella patens (Hedw.) B.S.G.
journal, January 1994

  • Reski, Ralf; Faust, Merle; Wang, Xiao-Hui
  • MGG Molecular & General Genetics, Vol. 244, Issue 4
  • DOI: 10.1007/BF00286686

Improved criteria and comparative genomics tool provide new insights into grass paleogenomics
journal, August 2009

  • Salse, J.; Abrouk, M.; Murat, F.
  • Briefings in Bioinformatics, Vol. 10, Issue 6
  • DOI: 10.1093/bib/bbp037

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation
journal, April 2010


PASTEC: An Automatic Transposable Element Classification Tool
journal, May 2014


Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
journal, January 2003


Engineering a software tool for gene structure prediction in higher organisms
journal, December 2005

  • Gremme, Gordon; Brendel, Volker; Sparks, Michael E.
  • Information and Software Technology, Vol. 47, Issue 15
  • DOI: 10.1016/j.infsof.2005.09.005

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


A plant DNA minipreparation: Version II
journal, September 1983

  • Dellaporta, Stephen L.; Wood, Jonathan; Hicks, James B.
  • Plant Molecular Biology Reporter, Vol. 1, Issue 4, p. 19-21
  • DOI: 10.1007/BF02712670

Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex
journal, January 2014

  • Beike, Anna K.; von Stackelberg, Mark; Schallenberg-Rüdinger, Mareike
  • BMC Evolutionary Biology, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2148-14-158

Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity
journal, January 2010

  • Lang, Daniel; Weiche, Benjamin; Timmerhaus, Gerrit
  • Genome Biology and Evolution, Vol. 2
  • DOI: 10.1093/gbe/evq032

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
journal, January 2012


Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011

  • Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
  • Nature Biotechnology, Vol. 29, Issue 7
  • DOI: 10.1038/nbt.1883

An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens
journal, January 2007

  • Rensing, Stefan A.; Ick, Julia; Fawcett, Jeffrey A.
  • BMC Evolutionary Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1471-2148-7-130

Epigenetic reprogramming in plant sexual reproduction
journal, July 2014

  • Kawashima, Tomokazu; Berger, Frédéric
  • Nature Reviews Genetics, Vol. 15, Issue 9
  • DOI: 10.1038/nrg3685

The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress
journal, June 2014

  • Widiez, Thomas; Symeonidi, Aikaterini; Luo, Chongyuan
  • The Plant Journal, Vol. 79, Issue 1
  • DOI: 10.1111/tpj.12542

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements
journal, April 2008


Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010


Widespread natural variation of DNA methylation within angiosperms
journal, September 2016


An overview of plant centromeres
journal, September 2009


Selection Is No More Efficient in Haploid than in Diploid Life Stages of an Angiosperm and a Moss
journal, May 2013

  • Szövényi, Péter; Ricca, Mariana; Hock, Zsófia
  • Molecular Biology and Evolution, Vol. 30, Issue 8
  • DOI: 10.1093/molbev/mst095

Mining EST databases to resolve evolutionary events in major crop species
journal, October 2004

  • Schlueter, Jessica A.; Dixon, Phillip; Granger, Cheryl
  • Genome, Vol. 47, Issue 5
  • DOI: 10.1139/g04-047

Origins, evolution, and phenotypic impact of new genes
journal, July 2010


The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants
journal, December 2007


The evolutionary significance of polyploidy
journal, May 2017

  • Van de Peer, Yves; Mizrachi, Eshchar; Marchal, Kathleen
  • Nature Reviews Genetics, Vol. 18, Issue 7
  • DOI: 10.1038/nrg.2017.26

Identifying ChIP-seq enrichment using MACS
journal, August 2012


A sequence-anchored genetic linkage map for the moss, Physcomitrella patens
journal, December 2008


Tandem repeats finder: a program to analyze DNA sequences
journal, January 1999


Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
journal, April 2011


SiZer for Exploration of Structures in Curves
journal, September 1999


Unique Tissue-Specific Cell Cycle in Physcomitrella
journal, January 2003


i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets
journal, November 2011

  • Proost, Sebastian; Fostier, Jan; De Witte, Dieter
  • Nucleic Acids Research, Vol. 40, Issue 2
  • DOI: 10.1093/nar/gkr955

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
journal, May 2014

  • Vanneste, Kevin; Baele, Guy; Maere, Steven
  • Genome Research, Vol. 24, Issue 8
  • DOI: 10.1101/gr.168997.113

The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

Genome duplication and the origin of angiosperms
journal, November 2005


Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
journal, January 2013


The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation
journal, January 2012


In silico archeogenomics unveils modern plant genome organisation, regulation and evolution
journal, April 2012


De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
journal, September 2014

  • Li, Ying-hui; Zhou, Guangyu; Ma, Jianxin
  • Nature Biotechnology, Vol. 32, Issue 10
  • DOI: 10.1038/nbt.2979

Conservation and divergence of methylation patterning in plants and animals
journal, April 2010

  • Feng, S.; Cokus, S. J.; Zhang, X.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 19
  • DOI: 10.1073/pnas.1002720107

Dehydration-responsive features of Atrichum undulatum
journal, June 2016


Highly efficient gene tagging in the bryophyte Physcomitrella patens using the tobacco ( Nicotiana tabacum ) Tnt1 retrotransposon
journal, August 2016

  • Vives, Cristina; Charlot, Florence; Mhiri, Corinne
  • New Phytologist, Vol. 212, Issue 3
  • DOI: 10.1111/nph.14152

An evolutionary case for functional gene body methylation in plants and animals
journal, May 2017


Developmental relaxation of transposable element silencing in plants: functional or byproduct?
journal, November 2012


The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
journal, July 2010


LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
journal, January 2008

  • Ellinghaus, David; Kurtz, Stefan; Willhoeft, Ute
  • BMC Bioinformatics, Vol. 9, Issue 1
  • DOI: 10.1186/1471-2105-9-18

Chromosomal histone modification patterns – from conservation to diversity
journal, April 2006


Transcriptional Control of Gene Expression by MicroRNAs
journal, January 2010


Plant sterols and the membrane environment
journal, May 1998


Whole-genome sequencing of multiple Arabidopsis thaliana populations
journal, August 2011

  • Cao, Jun; Schneeberger, Korbinian; Ossowski, Stephan
  • Nature Genetics, Vol. 43, Issue 10
  • DOI: 10.1038/ng.911

The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants
journal, May 2017


Analyses of transcriptome sequences reveal multiple ancient large‐scale duplication events in the ancestor of Sphagnopsida (Bryophyta)
journal, February 2016

  • Devos, Nicolas; Szövényi, Péter; Weston, David J.
  • New Phytologist, Vol. 211, Issue 1
  • DOI: 10.1111/nph.13887

PGSB PlantsDB: updates to the database framework for comparative plant genome research
journal, November 2015

  • Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai C.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1130

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea
journal, January 2016

  • Olsen, Jeanine L.; Rouzé, Pierre; Verhelst, Bram
  • Nature, Vol. 530, Issue 7590
  • DOI: 10.1038/nature16548

THE SPECIATION HISTORY OF THE PHYSCOMITRIUM-PHYSCOMITRELLA SPECIES COMPLEX
journal, January 2010


The Sequence Alignment/Map format and SAMtools
journal, June 2009


A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction
journal, January 2016


The PpCMT chromomethylase affects cell growth and interacts with the homolog of LIKE HETEROCHROMATIN PROTEIN 1 in the moss Physcomitrella patens
journal, January 2014

  • Dangwal, Meenakshi; Kapoor, Sanjay; Kapoor, Meenu
  • The Plant Journal, Vol. 77, Issue 4
  • DOI: 10.1111/tpj.12406

Plant genomes enclose footprints of past infections by giant virus relatives
journal, June 2014

  • Maumus, Florian; Epert, Aline; Nogué, Fabien
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5268

Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification
journal, July 2012

  • Vekemans, Dries; Proost, Sebastian; Vanneste, Kevin
  • Molecular Biology and Evolution, Vol. 29, Issue 12
  • DOI: 10.1093/molbev/mss183

Nuclear DNA content variation and evolution in liverworts
journal, September 2013

  • Bainard, Jillian D.; Forrest, Laura L.; Goffinet, Bernard
  • Molecular Phylogenetics and Evolution, Vol. 68, Issue 3
  • DOI: 10.1016/j.ympev.2013.04.008

Phytochromes: More Than Meets the Eye
journal, July 2016


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    journal, September 2018

    • Heer, Katrin; Ullrich, Kristian K.; Hiss, Manuel
    • Ecology and Evolution, Vol. 8, Issue 19
    • DOI: 10.1002/ece3.4374

    Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes
    journal, June 2019


    Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.)
    journal, July 2019


    Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)
    journal, May 2019


    Stable Co-Cultivation of the Moss Physcomitrella patens with Human Cells in vitro as a New Approach to Support Metabolism of Diseased Alzheimer Cells
    journal, July 2019

    • Zakirova, Elena Y.; Chastukhina, Inna B.; Valeeva, Lia R.
    • Journal of Alzheimer's Disease, Vol. 70, Issue 1
    • DOI: 10.3233/jad-190333

    Convergent evolution of hetero‐oligomeric cellulose synthesis complexes in mosses and seed plants
    journal, May 2019

    • Li, Xingxing; Speicher, Tori L.; Dees, Dianka C. T.
    • The Plant Journal
    • DOI: 10.1111/tpj.14366

    Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing
    journal, September 2018

    • Heer, Katrin; Ullrich, Kristian K.; Hiss, Manuel
    • Ecology and Evolution, Vol. 8, Issue 19
    • DOI: 10.1002/ece3.4374

    Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes
    journal, June 2019


    Convergent evolution of hetero‐oligomeric cellulose synthesis complexes in mosses and seed plants
    journal, May 2019

    • Li, Xingxing; Speicher, Tori L.; Dees, Dianka C. T.
    • The Plant Journal
    • DOI: 10.1111/tpj.14366

    Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.)
    journal, July 2019


    Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)
    journal, May 2019


    Stable Co-Cultivation of the Moss Physcomitrella patens with Human Cells in vitro as a New Approach to Support Metabolism of Diseased Alzheimer Cells
    journal, July 2019

    • Zakirova, Elena Y.; Chastukhina, Inna B.; Valeeva, Lia R.
    • Journal of Alzheimer's Disease, Vol. 70, Issue 1
    • DOI: 10.3233/jad-190333

    The hornwort genome and early land plant evolution
    journal, February 2020


    Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts
    journal, March 2020