title: The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
abstract: Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.
authors.affiliation: 1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [4].
authors.forename: Juliane C
authors.initials: JC
authors.lastname: Dohm
authors.affiliation: 1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [4].
authors.forename: André E
authors.initials: AE
authors.lastname: Minoche
authors.affiliation: Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany.
authors.forename: Daniela
authors.initials: D
authors.lastname: Holtgräwe
authors.affiliation: 1] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Salvador
authors.initials: S
authors.lastname: Capella-Gutiérrez
authors.affiliation: TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Zakrzewski
authors.affiliation: University of Leipzig, Department of Computer Science, Härtelstraße 16-18, 04107 Leipzig, Germany.
authors.forename: Hakim
authors.initials: H
authors.lastname: Tafer
authors.affiliation: Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Rupp
authors.affiliation: Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany.
authors.forename: Thomas Rosleff
authors.initials: TR
authors.lastname: Sörensen
authors.affiliation: Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Stracke
authors.affiliation: Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Köln, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.affiliation: Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.affiliation: Syngenta, Box 302, 26123 Landskrona, Sweden.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kraft
authors.affiliation: KWS SAAT AG, Grimsehlstraße 31, 37574 Einbeck, Germany.
authors.forename: Britta
authors.initials: B
authors.lastname: Schulz
authors.affiliation: University of Leipzig, Department of Computer Science, Härtelstraße 16-18, 04107 Leipzig, Germany.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmidt
authors.affiliation: 1] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.affiliation: Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Weisshaar
authors.affiliation: 1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Heinz
authors.initials: H
authors.lastname: Himmelbauer
mesh_terms: D027461:Beta vulgaris / Q000235:genetics*; D056804:Biofuels / Q000600:supply & distribution; D050260:Carbohydrate Metabolism; D032461:Chromosomes, Plant / Q000235:genetics; D018556:Crops, Agricultural / Q000235:genetics*; D000431:Ethanol / Q000378:metabolism; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D018724:Spinacia oleracea / Q000235:genetics
chemical_list: D056804:Biofuels; D000431:Ethanol