plantco.de - the Rensing lab pages

A main focus is the moss, Physcomitrella patens.
Methods encompass molecular and cellular biology, phylogeny, phylogenomics and comparative genomics.
In terms of systems biology we are interested in gene regulatory networks.
We are studying the evolution of plant interactions with fungi and bacteria to mutually exchange nutrients.

Our lab's research ranks 23rd in German plant science (source: Laborjournal)

General tools and resources

TAPscan - Comprehensive genome-wide classification reveals that many plant-specific transcription factors evolved in streptophyte algae
Wilhelmsson P.K., Mühlich C., Ullrich K.K., Rensing S.A. (2017) Genome Biology and Evolution, evx258
GTP and ATP2 - Green Targeting Predictor and Ambiguous mt/pt Targeting Predictor 2
Fuss J., Liegmann O., Krause K., Rensing S.A. (2013) New Phytol 200:1022
ATP - ambiguous mt/pt protein targeting predictor
Mitschke J., Fuss J., Blum T., Höglund A., Reski R., Kohlbacher O., Rensing S.A. (2009) Prediction of dual protein targeting to plant organelles. New Phytol 183:224
KeyS - software for paralog clustering and Ks distribution plots (please contact Stefan Rensing)
Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R (2007) An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol 7:130
PlanTAPDB - plant transcription associated proteins
Richardt S, Lang D, Reski R, Frank W and Rensing SA (2007) PlanTAPDB: A phylogeny-based resource of plant transcription associated proteins. Plant Physiol 143:1452-1466

P. patens resources and links

Gene model v3.3 annotation spreadsheet
Ecotype Reute pseudogenome sequence
The P. patens genome browser & other resources @

The P. patens genome @ JGI / NCBI
& more resources @ Physcobase / plant-biotech.net

Phylogenetic trees of several gene families
Rensing SA, Lang D, Zimmer AD et al. (2008) The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319:64-69

SSR markers and P. patens ecotypes
von Stackelberg M, Rensing SA and Reski R (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 6:9

SVM-based splice site prediction for P. patens
Rensing SA, Fritzowsky D, Lang D and Reski R (2005) Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens. BMC Genomics 6:43

P. patens UTR repeats
Rensing SA, Lang D and Reski R (2003) In silico prediction of UTR repeats using clustered EST data. In: Proceedings of the German Conference on Bioinformatics 2003, Mewes H-W, Heun V, Frishman D, Kramer S (eds.), pp 117-122, Belleville Verlag Michael Farin, Munich, Germany