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

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:
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
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
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)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; evolution; genome; chromosome; plant; moss; methylation; duplication; synteny; Physcomitrella patens
OSTI Identifier:
1439140
Alternate Identifier(s):
OSTI ID: 1456995

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., 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.. 2017. "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}
}

Works referenced in this record:

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