Assembly, mapping, annotation and analysis of a moss (Physcomitrella patens) genome
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.
(See online at https://dx.doi.org/10.1186/1471-2229-6-9) - 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.
(See online at https://dx.doi.org/10.1186/1471-2148-7-130) - 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.
(See online at https://dx.doi.org/10.1007/s00438-007-0257-6) - 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.
(See online at https://dx.doi.org/10.1104/pp.107.095760) - 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.
(See online at https://dx.doi.org/10.1073/pnas.0800864105) - 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.
(See online at https://dx.doi.org/10.1111/j.1365-313X.2008.03637.x) - 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.
(See online at https://dx.doi.org/10.1016/j.tplants.2008.07.002) - 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.
(See online at https://dx.doi.org/10.1126/science.1150646) - 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.
(See online at https://dx.doi.org/10.1111/j.1438-8677.2008.00174.x) - 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.
(See online at https://dx.doi.org/10.1093/mp/ssp076) - 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.
(See online at https://dx.doi.org/10.1186/1471-2148-9-126) - 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.
(See online at https://dx.doi.org/10.1093/gbe/evq032) - 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.
(See online at https://dx.doi.org/10.1186/1471-2229-10-76) - 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.
(See online at https://dx.doi.org/10.1007/s11103-009-9550-6) - 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.
(See online at https://doi.org/10.1093/bioinformatics/bts189)
