Assembly, mapping, annotation and analysis of a moss (Physcomitrella patens) genome

• Applicant: Professor Dr. Ralf Reski
• Subject Area: Plant Genetics and Genomics
• Term: from 2006 to 2011
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 18837657

• Final Report Year: 2012

Final Report Abstract

The genome of the moss "Physcomitrella patens" was sequenced with support of the US Department of Energy by their Joint Genome Institute (JGI) in California. At that time it was the first sequenced genome of a lower plant and the fourth plant genome at all. We spear-headed the world-wide attempts in genome assembly, annotation and analysis with our project. Our data was published in numerous scientific publications and via the web browser www.cosmoss.org which was significantly further developed in the frame of our project. This browser now is THE central resource world-wide for all genetic information about "Physcomitrella". In specialized international workshops we advised scientists from all over the world in the analysis and annotation of the moss genome. Due to the results of our project "Physcomitrella" is now generally accepted as a plant model species. This statement is underpinned by the fact that the JGI recently has chosen the "Physcomitrella" genome as one out of only five plant flagship genomes, the analysis of which will bring important information for global climate change and bioenergy. As bryophytes bridge the evolutionary gap of one billion years between algae and flowering plants we have enabled comparative evolutionary studies in plants at genome level.

Publications

• 2006. 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 Biology, Vol. 6.2006, 9.
  von Stackelberg, M., Rensing, S.A., and Reski, R.
  
• 2007. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evolutionary Biology, Vol. 7. 2007, 130.
  Rensing, S.A., Ick, J., Fawcett, J.A., Lang, D., Zimmer, A., Peer, Y.V. de, and Reski, R.
  
• 2007. Dating the early evolution of plants: detection and molecular clock analyses of orthologs. Molecular Genetics and Genomics, Vol. 278, pp. 393–402.
  Zimmer, A., Lang, D., Richardt, S., Frank, W., Reski, R., Rensing, S.A.
  
• 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiology, vol. 143. 2007, no. 4, pp. 1452-1466.
  Richardt, S., Lang, D., Reski, R., Frank, W., and Rensing, S.A.
  
• 2008. A PIIB-type Ca2+-ATPase is essential for stress adaptation in Physcomitrella patens. Proceedings of the National Academy of Sciences (USA), vol. 105. 2008, no. 49, pp. 19555–19560.
  Qudeimat, E., Faltusz, A.M.C., Wheeler, G., Lang, D., Holtorf, H., Brownlee, C., Reski, R., Frank, W.
  
• 2008. A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. The Plant Journal 56, 855-866. The Plant Journal, Vol. 56. 2008, Issue 5, pp. 855–866.
  Kamisugi, Y., Von Stackelberg, M., Lang, D., Care, M., Reski, R., Rensing, S.A., Cuming, A.C.
  
• 2008. Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends in Plant Science, Vol. 13. 2008, Issue 10, pp. 542–549.
  Lang, D., Zimmer, A.D., Rensing, S.A., and Reski, R.
  
• 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, Vol. 319.2008, Issue 5859, pp. 64-69.
  Rensing, S.A., Lang, D., Zimmer, A.D et al.
  
• 2009. A uniquely high number of ftsZ genes in the moss Physcomitrella patens. Plant Biology, Vol. 11. 2009, Issue 5, pp. 744–750.
  Martin, A., Lang, D., Heckmann, J., Zimmer, A.D., Vervliet-Scheebaum, M., and Reski, R.
  
• 2009. 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. Molecular Plant, Vol. 2. 2009, Issue 6, pp. 1359–1372.
  Martin, A., Lang, D., Hanke, S.T., Mueller, S.J.X., Sarnighausen, E., Vervliet-Scheebaum, M., Reski, R.
  
• 2009. The evolution of nuclear auxin signalling. BMC Evolutionary Biology, Vol. 9.2009: 126.
  Paponov, I., Teale, W., Lang, D., Paponov, M., Reski, R., Rensing, S., Palme, K.
  
• 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion and correlation with complexity. Genome Biology and Evolution, Vol. 2. 2010, pp. 488-503.
  Lang, D., Weiche, B., Timmerhaus, G., Richardt, S., Riaño-Pachón, D.M., Corrêa, L.G.G., Reski, R., Mueller-Roeber, B., Rensing, S.A.
  
• 2010. Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens. BMC Plant Biology, Vol. 10.2010: 76.
  Sinha, R., Zimmer, A.D., Bolte, K., Lang, D., Reski, R., Platzer, M., Rensing, S.A., and Backofen, R.
  
• 2010. Microarray analysis of the moss Physcomitrella patens reveals evolutionarily conserved transcriptional regulation of salt stress and abscisic acid signalling. Plant Molecular Biology, Vol. 72. 2010, pp. 27-45.
  Richardt, S., Timmerhaus, G., Lang, D., Qudeimat, E., Corrêa, L.G.G., Reski, R., Rensing, S.A., Frank, W.
  
• 2012. TSSi - An R Package for Transcription Start Site Identification from 5’ mRNA Tag Data. Bioinformatics, Vol. 28. 2012, Issue 12, pp. 1641-1642.
  Kreutz, C., Gehring, J.S., Lang, D., Reski, R., Timmer, J., and Rensing, S.A.