Genetics and Genomics of Physcomitrella patens

Living reference work entry
Part of the The Plant Sciences book series (PLANTSCI, volume 20)


For about a century, spanning the eras of early genetics to state-of-the-art biotechnology, the moss Physcomitrella patens has been a popular object of biological research. Meanwhile it has become an established model organism in plant evolutionary and developmental biology, mainly due to a combination of two factors: its phylogenetic key position in the plant tree of life and the sum of its favorable biological features. As a member of an early diverging land plant lineage – the bryophytes – Physcomitrella fills the gap between other models of the green lineage such as aquatic algae and flowering plants. The advantages of small stature and short generation cycles, accompanied by established and reliable cultivation techniques provide researchers with a robust, relatively fast, and easy cultivation for experiments in a laboratory environment. Precise genome engineering is enabled by the moss’s haploid-dominant lifestyle and its specifically high rate of homologous recombination during DNA repair, that is routinely utilized through an extensive molecular toolkit for efficient gene targeting since 1998. Physcomitrella’s genome was sequenced about a decade ago, making it the first bryophyte and even one of the first plants to be chosen for such a whole-genome shotgun sequencing approach. Ever since, the annotation of this “flagship genome” has been subject to constant improvement by an active community through the internet resource which provides a central platform for knowledge exchange as well as bioinformatics data and tools.


Physcomitrella patens Bryophyte Funariaceae Haploid dominance Forward genetics Reverse genetics Homologous recombination Gene targeting Knockin Knockout Gene silencing RNAi miRNA Transcriptome Genome Genome annotation Land plant evolution Genetic map Polyploidization 


  1. Allen CE. A chromosome difference correlated with sex differences in Sphaerocarpos. Science. 1917;46:466–7.CrossRefPubMedGoogle Scholar
  2. Arif MA, Frank W, Khraiwesh B. Role of RNA interference (RNAi) in the moss Physcomitrella patens. Int J Mol Sci. 2013;14:1516–40.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Ashton NW, Champagne CEM, Weiler T, Verkoczy LK. The bryophyte Physcomitrella patens replicates extrachromosomal transgenic elements. New Phytol. 2000;146:391–402.CrossRefGoogle Scholar
  4. Axtell MJ. The small RNAs of Physcomitrella patens: expression, function and evolution. In: Knight CD, Perroud P-F, Cove DJ, editors. Annual plant reviews volume 36: the moss Physcomitrella patens. Oxford, UK: Wiley-Blackwell; 2009. p. 113–142.Google Scholar
  5. Beike AK, von Stackelberg M, Schallenberg-Rüdinger M, Hanke ST, Follo M, Quandt D, McDaniel SF, Reski R, Tan BC, Rensing SA. Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex. BMC Evol Biol. 2014;14:158.CrossRefPubMedPubMedCentralGoogle Scholar
  6. Beike AK, Lang D, Zimmer AD, Wüst F, Trautmann D, Wiedemann G, Beyer P, Decker EL, Reski R. Insights from the cold transcriptome of Physcomitrella patens: global specialization pattern of conserved transcriptional regulators and identification of orphan genes involved in cold acclimation. New Phytol. 2015;205:869–81.CrossRefPubMedGoogle Scholar
  7. Coruh C, Cho SH, Shahid S, Liu Q, Wierzbicki A, Axtell MJ. Comprehensive annotation of Physcomitrella patens small RNA loci reveals that the heterochromatic short interfering RNA pathway is largely conserved in land plants. Plant Cell. 2015;27:2148–62.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Cove DJ, Perroud P-F, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Transformation of the moss Physcomitrella patens using T-DNA mutagenesis. Cold Spring Harb Protoc. 2009; doi:10.1101/pdb.prot5144.Google Scholar
  9. Cuming AC, Cho SH, Kamisugi Y, Graham H, Quatrano RS. Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss Physcomitrella patens. New Phytol. 2007;176:275–87.CrossRefPubMedGoogle Scholar
  10. Egener T, Granado J, Guitton M-C, Hohe A, Holtorf H, Lucht J, Rensing S, Schlink K, Schulte J, Schween G, Zimmermann S, Duwenig E, Rak B, Reski R. High frequency of phenotypic deviations in Physcomitrella patens plants transformed with a gene-disruption library. BMC Plant Biol. 2002;2:6.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Engel P. The induction of biochemical and morphological mutants in the moss Physcomitrella patens. Am J Bot. 1968;55:438–46.CrossRefGoogle Scholar
  12. Feschotte C, Jiang N, Wessler SR. Plant transposable elements: where genetics meets genomics. Nat Rev Genet. 2002;3:329–41.CrossRefPubMedGoogle Scholar
  13. Heitz E. Das Heterochromatin der Moose. I Jahrb Wiss Bot. 1928;69:762–818.Google Scholar
  14. Hiss M, Laule O, Meskauskiene RM, Arif MA, Decker EL, Erxleben A, Frank W, Hanke ST, Lang D, Martin A, Neu C, Reski R, Richardt S, Schallenberg-Rüdinger M, Szövényi P, Tiko T, Wiedemann G, Wolf L, Zimmermann P, Rensing SA. Large-scale gene expression profiling data for the model moss Physcomitrella patens aid understanding of developmental progression, culture and stress conditions. Plant J. 2014;79:530–9.CrossRefPubMedGoogle Scholar
  15. Horst NA, Katz A, Pereman I, Decker EL, Ohad N, Reski R. A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction. Nature Plant. 2016;2:15209.CrossRefGoogle Scholar
  16. Hwang H-W, Wentzel EA, Mendell JT. A hexanucleotide element directs microRNA nuclear import. Science. 2007;315:97–100.CrossRefPubMedGoogle Scholar
  17. Kamisugi Y, von Stackelberg M, Lang D, Care M, Reski R, Rensing SA, Cuming AC. A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. Plant J. 2008;56:855–66.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Khraiwesh B, Ossowski S, Weigel D, Reski R, Frank W. Specific gene silencing by artificial MicroRNAs in Physcomitrella patens: an alternative to targeted gene knockouts. Plant Physiol. 2008;148:684–93.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, Frank W. Transcriptional control of gene expression by microRNAs. Cell. 2010;140:111–22.CrossRefPubMedGoogle Scholar
  20. Knapp E. Zur Genetik von Sphaerocarpus. Ber Dtsch Bot Ges. 1936;54:58–69.Google Scholar
  21. Lang D, Zimmer AD, Rensing SA, Reski R. Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends Plant Sci. 2008;13:542–9.CrossRefPubMedGoogle Scholar
  22. Lang D, Weiche B, Timmerhaus G, Richardt S, Riaño-Pachón DM, Corrêa LGG, Reski R, Mueller-Roeber B, Rensing SA. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2010;2:488–503.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Lujambio A, Lowe SW. The microcosmos of cancer. Nature. 2012;482:347–55.CrossRefPubMedPubMedCentralGoogle Scholar
  24. Martin A, Lang D, Hanke ST, Mueller SJX, Sarnighausen E, Vervliet-Scheebaum M, Reski R. Targeted gene knockouts reveal overlapping functions of the five Physcomitrella patens FtsZ isoforms in chloroplast division, chloroplast shaping, cell patterning, plant development, and gravity sensing. Mol Plant. 2009;2:1359–72.CrossRefPubMedPubMedCentralGoogle Scholar
  25. McDaniel SF, von Stackelberg M, Richardt S, Quatrano RS, Reski R, Rensing SA. The speciation history of the Physcomitrium-Physcomitrella species complex. Evolution. 2010;64:217–31.CrossRefPubMedGoogle Scholar
  26. Nakaoka Y, Miki T, Fujioka R, Uehara R, Tomioka A, Obuse C, Kubo M, Hiwatashi Y, Goshima G. An inducible RNA interference system in Physcomitrella patens reveals a dominant role of augmin in phragmoplast microtubule generation. Plant Cell. 2012;24:1478–93.CrossRefPubMedPubMedCentralGoogle Scholar
  27. Nishiyama T, Hiwatashi Y, Sakakibara I, Kato M, Hasebe M. Tagged mutagenesis and gene-trap in the moss, Physcomitrella patens by shuttle mutagenesis. DNA Res. 2000;7:9–17.CrossRefPubMedGoogle Scholar
  28. Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KDE, Wolf PG, Duffy AM, Karol KG. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC Genomics. 2010;11:143.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Prigge MJ, Lavy M, Ashton NW, Estelle M. Physcomitrella patens auxin-resistant mutants affect conserved elements of an auxin-signaling pathway. Curr Biol. 2010;20:1907–12.CrossRefPubMedGoogle Scholar
  30. Rensing SA, Rombauts S, Van de Peer Y, Reski R. Moss transcriptome and beyond. Trends Plant Sci. 2002a;7:535–8.CrossRefPubMedGoogle Scholar
  31. Rensing SA, Rombauts S, Hohe A, Lang D, Duwenig E, Rouze P, Van de Peer Y, Reski R. The transcriptome of the moss Physcomitrella patens: comparative analysis reveals a rich source of new genes. 2002b. Accessed 26 Aug 2015.
  32. Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol. 2007;7:130.CrossRefPubMedPubMedCentralGoogle Scholar
  33. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud P-F, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S-I, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu S-H, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008;319:64–9.CrossRefPubMedGoogle Scholar
  34. Rensing SA, Lang D, Zimmer AD. Comparative genomics. In: Knight CD, Perroud P-F, Cove DJ, editors. Annual plant reviews volume 36: the moss Physcomitrella patens. Oxford, UK: Wiley-Blackwell; 2009. p. 42–75.Google Scholar
  35. Rensing SA, Beike AK, Lang D. Evolutionary importance of generative polyploidy for genome evolution of haploid-dominant land plants. In: Leitch IJ, Greilhuber J, Dolezel J, Wendel JF, editors. Plant genome diversity, vol. 2. Wien: Springer; 2013. p. 295–305.CrossRefGoogle Scholar
  36. Reski R. Physcomitrella and Arabidopsis: the David and Goliath of reverse genetics. Trends Plant Sci. 1998;3:209–10.CrossRefGoogle Scholar
  37. Reski R, Faust M, Wang X-H, Wehe M, Abel W. Genome analysis of the moss Physcomitrella patens (Hedw.) B.S.G. Mol Gen Genet. 1994;244:352–9.CrossRefPubMedGoogle Scholar
  38. Reski R, Parsons J, Decker EL. Moss-made pharmaceuticals: from bench to bedside. Plant Biotechnol J. 2015;13:1191–8.CrossRefPubMedPubMedCentralGoogle Scholar
  39. Richardt S, Timmerhaus G, Lang D, Qudeimat E, Corrêa LGG, Reski R, Rensing SA, Frank W. Microarray analysis of the moss Physcomitrella patens reveals evolutionarily conserved transcriptional regulation of salt stress and abscisic acid signalling. Plant Mol Biol. 2010;72:27–45.CrossRefPubMedGoogle Scholar
  40. Schaefer DG, Zryd J-P. Efficient gene targeting in the moss Physcomitrella patens. Plant J. 1997;11:1195–206.CrossRefPubMedGoogle Scholar
  41. Schaefer D, Zryd J-P, Knight CD, Cove DJ. Stable transformation of the moss Physcomitrella patens. Mol Gen Genet. 1991;226:418–24.CrossRefPubMedGoogle Scholar
  42. Schween G, Gorr G, Hohe A, Reski R. Unique tissue-specific cell cycle in Physcomitrella. Plant Biol. 2003;5:50–8.CrossRefGoogle Scholar
  43. Schween G, Egener T, Fritzowsky D, Granado J, Guitton M-C, Hartmann N, Hohe A, Holtorf H, Lang D, Lucht JM, Reinhard C, Rensing SA, Schlink K, Schulte J, Reski R. Large-scale analysis of 73 329 Physcomitrella plants transformed with different gene disruption libraries: production parameters and mutant phenotypes. Plant Biol. 2005;7:228–37.CrossRefPubMedGoogle Scholar
  44. Stehlin HG. Remarques sur les faunules de mammifères des couches éocènes et oligocènes du Bassin de Paris. B Soc Geol Fr. 1909;9:488–520.Google Scholar
  45. Strepp R, Scholz S, Kruse S, Speth V, Reski R. Plant nuclear gene knockout reveals a role in plastid division for the homolog of the bacterial cell division protein FtsZ, an ancestral tubulin. Proc Natl Acad Sci. 1998;95:4368–73.CrossRefPubMedPubMedCentralGoogle Scholar
  46. Strotbek C, Krinninger S, Frank W. The moss Physcomitrella patens: methods and tools from cultivation to targeted analysis of gene function. Int J Dev Biol. 2013;57:553–64.CrossRefPubMedGoogle Scholar
  47. Sugita M, Aoki S. Chloroplasts. In: Knight CD, Perroud P-F, Cove DJ, editors. Annual plant reviews volume 36: the moss Physcomitrella patens. Oxford, UK: Wiley-Blackwell; 2009. p. 182–210.Google Scholar
  48. Sugiura C, Sugita M. Plastid transformation reveals that moss tRNA(Arg)-CCG is not essential for plastid function. Plant J. 2004;40:314–21.CrossRefPubMedGoogle Scholar
  49. Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M. Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Res. 2003;31:5324–31.CrossRefPubMedPubMedCentralGoogle Scholar
  50. Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N. The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol. 2007;24:699–709.CrossRefPubMedGoogle Scholar
  51. Von Stackelberg M, Rensing SA, Reski R. Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. BMC Plant Biol. 2006;6:9.CrossRefPubMedPubMedCentralGoogle Scholar
  52. Von Wettstein F. Über plasmatische Vererbung und über das Zusammenwirken von Genen und Plasma. Ber Dtsch Bot Ges. 1928;46:32–49.Google Scholar
  53. Wolf L, Rizzini L, Stracke R, Ulm R, Rensing SA. The molecular and physiological responses of Physcomitrella patens to ultraviolet-B radiation. Plant Physiol. 2010;153:1123–34.CrossRefPubMedPubMedCentralGoogle Scholar
  54. Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, Van de Peer Y, Rensing SA, Reski R. Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics. 2013;14:498.CrossRefPubMedPubMedCentralGoogle Scholar

Further Readings

  1. Cove, D. The moss Physcomitrella patens. Annu Rev. Genet 2005;39:339–358.CrossRefPubMedGoogle Scholar
  2. Cove DJ, Cuming AC. Genetics and genomics of moss models: physiology enters the twenty-first century. In: Hanson DT, Rice SK, editors. Photosynthesis in bryophytes and early land plants. Dordrecht: Springer; 2013. p. 187–199.Google Scholar
  3. Knight C, Perroud PF, Cove D. Annual plant reviews volume 36: the moss Physcomitrella patens. Oxford, UK: Wiley-Blackwell; 2009.Google Scholar
  4. Strotbek, C., S. Krinninger, and W. Frank. The moss Physcomitrella patens: methods and tools from cultivation to targeted analysis of gene function. Int J Dev Biol 2013;57:553–564.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Plant Biotechnology, Faculty of BiologyUniversity of FreiburgFreiburgGermany
  2. 2.FRIAS – Freiburg Institute for Advanced StudiesFreiburgGermany
  3. 3.BIOSS – Centre for Biological Signalling StudiesFreiburgGermany

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