The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

W. Wang, G. Haberer, H. Gundlach, C. Gläßer, T. Nussbaumer, M.C. Luo, A. Lomsadze, M. Borodovsky, R.A. Kerstetter, J. Shanklin, D.W. Byrant, T.C. Mockler, K.J. Appenroth, J. Grimwood, J. Jenkins, J. Chow, C. Choi, C. Adam, X.-H. Cao, J. Fuchs, I. Schubert, D. Rokhsar, J. Schmutz, T.P. Michael, K.F.X. Mayer and J Messing ()
Additional contact information
W. Wang: Waksman Institute of Microbiology, Rutgers University
G. Haberer: MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH)
H. Gundlach: MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH)
C. Gläßer: MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH)
T. Nussbaumer: MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH)
M.C. Luo: University of California
A. Lomsadze: Georgia Institute of Technology
M. Borodovsky: Georgia Institute of Technology
R.A. Kerstetter: Waksman Institute of Microbiology, Rutgers University
J. Shanklin: Brookhaven National Laboratory
D.W. Byrant: Donald Danforth Plant Science Center
T.C. Mockler: Donald Danforth Plant Science Center
K.J. Appenroth: University of Jena
J. Grimwood: DOE Joint Genome Institute
J. Jenkins: HudsonAlpha Institute for Biotechnology
J. Chow: DOE Joint Genome Institute
C. Choi: DOE Joint Genome Institute
C. Adam: DOE Joint Genome Institute
X.-H. Cao: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)
J. Fuchs: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)
I. Schubert: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)
D. Rokhsar: DOE Joint Genome Institute
J. Schmutz: DOE Joint Genome Institute
T.P. Michael: Waksman Institute of Microbiology, Rutgers University
K.F.X. Mayer: MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH)
J Messing: Waksman Institute of Microbiology, Rutgers University

Nature Communications, 2014, vol. 5, issue 1, 1-13

Abstract: Abstract The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

Date: 2014
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DOI: 10.1038/ncomms4311

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