Physcomitrella patens

Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Moss Superclass V; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella

Introduction

The moss Physcomitrella patens is the first Bryophyte genome to be sequenced. Bryophytes, comprising hornworts, mosses and liverworts, occupy an ideal phylogenetic position - halfway between algae and seed plants, for studying the evolutionary history of plants.

Physcomitrella patens has emerged as a model plant because of its high homologous recombination frequency that enables efficient gene targeting, and also its relatively simple morphology and its small genome size (~500Mb). Mosses are considered to be the first land plants that evolved about 450 million years ago, and the sequencing of the Physcomitrella genome will enlighten the adaptive changes that enabled the colonization of land by plants. The genome was sequenced by the Joint Genome Institute (JGI).

Our involvement

Our main contribution was the analyses we did on gene and genome duplication. Our analyses indicated that a recent large scale duplication, possibly involving the whole genome, indeed occurred in the evolutionary history of Physcomitrella patens, supporting previous EST-based suggestions. We also helped in assessing and improving the gene predictions.

In collaboration with:

Publications

2013

Zimmer, A., Lang, D., Buchta, K., Rombauts, S., Nishiyama, T., Hasebe, M., Van de Peer, Y., Rensing, S.A., Reski, R. (2013) 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 14:498.

2012

Van de Peer, Y., Pires, J.C. (2012) Getting up to speed. Curr. Opin. Plant Biol. 15(2):111-4.

2008

Rensing, S.A., Lang, D., Zimmer, A., Terry, A., Salamov, A., H,Shapiro, , Nishiyama, T., P.-Perroud, F., Lindquist, E., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K., Shin-I, T., Kuroki, Y., Toyoda, A., Suzuki, Y., S.-Hashimoto, I., Yamaguchi, K., Sugano, S., Kohara, Y., Fujiyama, A., Ashton, N., Anterola, A., Aoki, S., Barbazuk, W.B., Barker, E., Bennetzen, J., Blankenship, R., Cho, S.H., Dutcher, S., Estelle, M., Fawcett, J., Gundlach, H., Hanada, K., Heyl, A., Hicks, K. A., Hughes, J., Lohr, M., Mayer, K., Melkozernov, A., Murata, T., Nelson, D.R., Pils, B., Prigge, M., Reiss, B., Renner, T., Rombauts, S., Rushton, P., Sanderfoot, A., Schween, G., S.-Shiu, H., Stueber, K., Theodoulou, F.L., Tu, H., Van de Peer, Y., Verrier, P.J., Waters, E., Wood, A., Yang, G., Cove, D., Cuming, A.C., Hasebe, M., Lucas, S., Mishler, B.D., Reski, R., Grigoriev, I., Quatrano, R.S., Boore, J.L. (2008) The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319(5859):64-9.

2007

Rensing, S.A., Ick, J., Fawcett, J., 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.

2002

Rensing, S.A., Rombauts, S., Van de Peer, Y., Reski, R. (2002) Moss transcriptome and beyond. Trends Plant Science 7(12):535-8.

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Bioinformatics & Evolutionary Genomics
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