title: The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.
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.
authors.affiliation: 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2].
authors.forename: W
authors.initials: W
authors.lastname: Wang
authors.affiliation: 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2].
authors.forename: G
authors.initials: G
authors.lastname: Haberer
authors.affiliation: 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2].
authors.forename: H
authors.initials: H
authors.lastname: Gundlach
authors.affiliation: 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2].
authors.forename: C
authors.initials: C
authors.lastname: Gläßer
authors.affiliation: MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Nussbaumer
authors.affiliation: Department of Plant Sciences, University of California, 265 Hunt Hall, One Shields Avenue, Davis, California 95616, USA.
authors.forename: M C
authors.initials: MC
authors.lastname: Luo
authors.affiliation: Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA.
authors.forename: A
authors.initials: A
authors.lastname: Lomsadze
authors.affiliation: Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA.
authors.forename: M
authors.initials: M
authors.lastname: Borodovsky
authors.affiliation: 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2].
authors.forename: R A
authors.initials: RA
authors.lastname: Kerstetter
authors.affiliation: Brookhaven National Laboratory, 50 Bell Ave, Upton, New York 11973, USA.
authors.forename: J
authors.initials: J
authors.lastname: Shanklin
authors.affiliation: Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA.
authors.forename: D W
authors.initials: DW
authors.lastname: Byrant
authors.affiliation: Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA.
authors.forename: T C
authors.initials: TC
authors.lastname: Mockler
authors.affiliation: Department of Plant Physiology, University of Jena, Dornburger Str. 159, 07743 Jena, Germany.
authors.forename: K J
authors.initials: KJ
authors.lastname: Appenroth
authors.affiliation: 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA.
authors.forename: J
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA.
authors.forename: J
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: J
authors.initials: J
authors.lastname: Chow
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: C
authors.initials: C
authors.lastname: Choi
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: C
authors.initials: C
authors.lastname: Adam
authors.affiliation: Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany.
authors.forename: X-H
authors.initials: XH
authors.lastname: Cao
authors.affiliation: Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Fuchs
authors.affiliation: Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany.
authors.forename: I
authors.initials: I
authors.lastname: Schubert
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: D
authors.initials: D
authors.lastname: Rokhsar
authors.affiliation: 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA.
authors.forename: J
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2].
authors.forename: T P
authors.initials: TP
authors.lastname: Michael
authors.affiliation: MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
authors.forename: K F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA.
authors.forename: J
authors.initials: J
authors.lastname: Messing
mesh_terms: D029064:Araceae / Q000235:genetics* / Q000254:growth & development*; D005618:Fresh Water; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data