The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Rosleff Sörensen T, Stracke R, Reinhardt R, Goesmann A, et al. (2014)
Nature 505(7484): 546-549.

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: 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.
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Dohm JC, Minoche AE, Holtgräwe D, et al. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 2014;505(7484):546-549.
Dohm, J. C., Minoche, A. E., Holtgräwe, D., Capella-Gutiérrez, S., Zakrzewski, F., Tafer, H., Rupp, O., et al. (2014). The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature, 505(7484), 546-549. doi:10.1038/nature12817
Dohm, J. C., Minoche, A. E., Holtgräwe, D., Capella-Gutiérrez, S., Zakrzewski, F., Tafer, H., Rupp, O., Rosleff Sörensen, T., Stracke, R., Reinhardt, R., et al. (2014). The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505, 546-549.
Dohm, J.C., et al., 2014. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature, 505(7484), p 546-549.
J.C. Dohm, et al., “The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)”, Nature, vol. 505, 2014, pp. 546-549.
Dohm, J.C., Minoche, A.E., Holtgräwe, D., Capella-Gutiérrez, S., Zakrzewski, F., Tafer, H., Rupp, O., Rosleff Sörensen, T., Stracke, R., Reinhardt, R., Goesmann, A., Kraft, T., Schulz, B., Stadler, P.F., Schmidt, T., Gabaldón, T., Lehrach, H., Weisshaar, B., Himmelbauer, H.: The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 505, 546-549 (2014).
Dohm, Juliane C, Minoche, André E, Holtgräwe, Daniela, Capella-Gutiérrez, Salvador, Zakrzewski, Falk, Tafer, Hakim, Rupp, Oliver, Rosleff Sörensen, Thomas, Stracke, Ralf, Reinhardt, Richard, Goesmann, Alexander, Kraft, Thomas, Schulz, Britta, Stadler, Peter F, Schmidt, Thomas, Gabaldón, Toni, Lehrach, Hans, Weisshaar, Bernd, and Himmelbauer, Heinz. “The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)”. Nature 505.7484 (2014): 546-549.
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PMID: 26890886
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PMID: 26463996
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PMID: 26647370
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PMID: 26616024
Evidence for a Common Origin of Homomorphic and Heteromorphic Sex Chromosomes in Distinct Spinacia Species.
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PMID: 26048564
The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal.
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PMID: 25071079
The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation.
Zakrzewski F, Schubert V, Viehoever P, Minoche AE, Dohm JC, Himmelbauer H, Weisshaar B, Schmidt T., Plant J. 78(6), 2014
PMID: 24661787

46 References

Data provided by Europe PubMed Central.

Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
Stanke M, Diekhans M, Baertsch R, Haussler D., Bioinformatics 24(5), 2008
PMID: 18218656
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW., Nucleic Acids Res. 35(9), 2007
PMID: 17452365

Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A., Nucleic Acids Res. 41(Database issue), 2013
PMID: 23125362
Plant snoRNA database.
Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Huttenhofer A, Kastenmayer JP, Green PJ, Shaw P, Marshall DF., Nucleic Acids Res. 31(1), 2003
PMID: 12520043
GenBank: update.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681350
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
Wehe A, Bansal MS, Burleigh JG, Eulenstein O., Bioinformatics 24(13), 2008
PMID: 18474508
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O., Syst. Biol. 59(3), 2010
PMID: 20525638
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH., Nucleic Acids Res. 40(7), 2012
PMID: 22217600
Reorganizing the protein space at the Universal Protein Resource (UniProt).
UniProt Consortium, Apweiler R, Jesus Martin M, O'onovan C, Magrane M, Alam-Faruque Y, Antunes R, Barrera Casanova E, Bely B, Bingley M, Bower L, Bursteinas B, Mun Chan W, Chavali G, Da Silva A, Dimmer E, Eberhardt R, Fazzini F, Fedotov A, Garavelli J, Castro LG, Gardner M, Hieta R, Huntley R, Jacobsen J, Legge D, Liu W, Luo J, Orchard S, Patient S, Pichler K, Poggioli D, Pontikos N, Pundir S, Rosanoff S, Sawford T, Sehra H, Turner E, Wardell T, Watkins X, Corbett M, Donnelly M, van Rensburg P, Goujon M, McWilliam H, Lopez R, Xenarios I, Bougueleret L, Bridge A, Poux S, Redaschi N, Argoud-Puy G, Auchincloss A, Axelsen K, Baratin D, Blatter MC, Boeckmann B, Bolleman J, Bollondi L, Boutet E, Braconi Quintaje S, Breuza L, deCastro E, Cerutti L, Coudert E, Cuche B, Cusin I, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gehant S, Ferro S, Gasteiger E, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Hulo N, James J, Jimenez S, Jungo F, Kappler T, Keller G, Lara V, Lemercier P, Lieberherr D, Martin X, Masson P, Moinat M, Morgat A, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stanley E, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey AL, Wu CH, Arighi CN, Arminski L, Barker WC, Chen C, Chen Y, Dubey P, Huang H, Kukreja A, Laiho K, Mazumder R, McGarvey P, Natale DA, Natarajan TG, Roberts NV, Suzek BE, Vinayaka C, Wang Q, Wang Y, Yeh LS, Zhang J., Nucleic Acids Res. 40(Database issue), 2012
PMID: 22102590
KEGG for integration and interpretation of large-scale molecular data sets.
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M., Nucleic Acids Res. 40(Database issue), 2012
PMID: 22080510
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
A genome-wide comparison of NB-LRR type of resistance gene analogs (RGA) in the plant kingdom.
Kim J, Lim CJ, Lee BW, Choi JP, Oh SK, Ahmad R, Kwon SY, Ahn J, Hur CG., Mol. Cells 33(4), 2012
PMID: 22453776
InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY., Nucleic Acids Res. 40(Database issue), 2012
PMID: 22096229
Dynamo maker ready to roll.
Young S., Nature 480(7376), 2011
PMID: 22158219
Sucrose transporters of higher plants.
Kuhn C, Grof CP., Curr. Opin. Plant Biol. 13(3), 2010
PMID: 20303321


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