Publication Date:
2013-12-20
Description:
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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dohm, Juliane C -- Minoche, Andre E -- Holtgrawe, Daniela -- Capella-Gutierrez, Salvador -- Zakrzewski, Falk -- Tafer, Hakim -- Rupp, Oliver -- Sorensen, Thomas Rosleff -- Stracke, Ralf -- Reinhardt, Richard -- Goesmann, Alexander -- Kraft, Thomas -- Schulz, Britta -- Stadler, Peter F -- Schmidt, Thomas -- Gabaldon, Toni -- Lehrach, Hans -- Weisshaar, Bernd -- Himmelbauer, Heinz -- England -- Nature. 2014 Jan 23;505(7484):546-9. doi: 10.1038/nature12817. Epub 2013 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉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]. ; Bielefeld University, CeBiTec and Department of Biology, Universitatsstrasse 25, 33615 Bielefeld, Germany. ; 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. ; TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany. ; University of Leipzig, Department of Computer Science, Hartelstrasse 16-18, 04107 Leipzig, Germany. ; Max Planck Genome Centre Cologne, Carl-von-Linne-Weg 10, 50829 Koln, Germany. ; Syngenta, Box 302, 26123 Landskrona, Sweden. ; KWS SAAT AG, Grimsehlstrasse 31, 37574 Einbeck, Germany. ; 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] Institucio Catalana de Recerca i Estudis Avancats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain. ; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. ; 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.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24352233" target="_blank"〉PubMed〈/a〉
Keywords:
Beta vulgaris/*genetics
;
Biofuels/supply & distribution
;
Carbohydrate Metabolism
;
Chromosomes, Plant/genetics
;
Crops, Agricultural/*genetics
;
Ethanol/metabolism
;
Genome, Plant/*genetics
;
Genomics
;
In Situ Hybridization, Fluorescence
;
Molecular Sequence Data
;
Phylogeny
;
Sequence Analysis, DNA
;
Spinacia oleracea/genetics
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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