Main Publications

  • Genomic distances reveal relationships of wild and cultivated beets

    Wascher FL, Stralis-Pavese N, McGrath JM, Schulz B, Himmelbauer H, Dohm JC. Nat Commun. 2022 Apr 19;13(1):2021

    Cultivated beets (Beta vulgaris ssp. vulgaris), including sugar beet, rank among the most important crops. The wild ancestor of beet crops is the sea beet Beta vulgaris ssp. maritima. Species and subspecies of wild beets are readily crossable with cultivated beets and are thus available for crop improvement. To study genomic relationships in the genus Beta, we sequence and analyse 606 beet genomes, encompassing sugar beet, sea beet, B. v. adanensis, B. macrocarpa, and B. patula. We observe... Read more

  • Assembly and characterization of the genome of chard (Beta vulgaris ssp. vulgaris var. cicla)

    Lehner R, Blazek L, Minoche AE, Dohm JC, Himmelbauer H. J Biotechnol. 2021 Jun 10;333:67-76

    Chard (Beta vulgaris ssp. vulgaris var. cicla) is a member of one of four different cultigroups of beets. While the genome of sugar beet, the most prominent beet crop, has been studied extensively, molecular data on other beet cultivars is scant. Here, we present a genome assembly of chard, a vegetable crop grown for its fleshy leaves. We report a de novo genome assembly of 604 Mbp, slightly larger than sugar beet assemblies presented so far. About 57 % of the assembly was... Read more

  • Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima

    Rodríguez Del Río Á, Minoche AE, Zwickl NF, Friedrich A, Liedtke S, Schmidt T, Himmelbauer H, Dohm JC. Plant J. 2019 Sep;99(6):1242-1253

    We present draft genome assemblies of Beta patula, a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related Beta vulgaris ssp. maritima (sea beet). Evidence-based reference gene sets for B. patula and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon B. vulgaris ssp. vulgaris (sugar beet). Large syntenic regions... Read more

  • Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

    Minoche AE, Dohm JC, Schneider J, Holtgräwe D, Viehöver P, Montfort M, Sörensen TR, Weisshaar B, Himmelbauer H. Genome Biol. 2015 Sep 2;16:184

    We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first... Read more

  • 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, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H. Nature. 2014 Jan 23;505(7484):546-9

    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 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... Read more

  • Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris)

    Dohm JC, Lange C, Holtgräwe D, Rosleff Sörensen T, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H. Plant J. 2012 May;70(3):528-40

    Sugar beet (Beta vulgaris) is an important crop plant accounting for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons, and genomic characterization of sugar beet is essential in order to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps covering all nine chromosomes. Based on this information we identified... Read more

Related Publications

  • Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes

    Capistrano-Gossmann GG, Ries D, Holtgräwe D, Minoche A, Kraft T, Frerichmann SLM, Rosleff Soerensen T, Dohm JC, González I, Schilhabel M, Varrelmann M, Tschoep H, Uphoff H, Schütze K, Borchardt D, Toerjek O, Mechelke W, Lein JC, Schechert AW, Frese L, Himmelbauer H, Weisshaar B, Kopisch-Obuch FJ. Nat Commun. 2017 Jun 6;8:15708

    Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated... Read more

  • Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris).

    Holtgräwe D, Sörensen TR, Viehöver P, Schneider J, Schulz B, Borchardt D, Kraft T, Himmelbauer H, Weisshaar B. PLoS One. 2014 Oct 10;9(10):e110113

    Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that... Read more

  • Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes

    Dohm JC, Lange C, Reinhardt R, Himmelbauer H. Plant J. 2009 Jan;57(1):14-26

    We characterized two overlapping sugar beet (Beta vulgaris) bacterial artificial chromosome (BAC) clones representing different haplotypes. A total of 254 kbp of the genomic sequence was determined of which the two BACs share 92 kbp. Eleven of 15 genes discovered in the sequenced interval locate to the overlap region. The haplotypes differ in exons by 1% (nucleotide level) and in non-coding regions by... Read more

  • Construction and characterization of a sugar beet (Beta vulgaris) fosmid library

    Lange C, Holtgräwe D, Schulz B, Weisshaar B, Himmelbauer H. Genome. 2008 Nov;51(11):948-51

    A sugar beet (Beta vulgaris) fosmid library from the doubled haploid accession KWS2320 encompassing 115,200 independent clones was constructed and characterized. The average insert size of the fosmid library was determined by pulsed field gel electrophoresis to be 39 kbp on average, thus representing 5.9-fold coverage of the sugar beet genome (758 Mbp). PCR screening of plate pools with primer pairs... Read more

  • Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes.

    Schneider K, Kulosa D, Soerensen TR, Möhring S, Heine M, Durstewitz G, Polley A, Weber E, Jamsari, Lein J, Hohmann U, Tahiro E, Weisshaar B, Schulz B, Koch G, Jung C, Ganal M. Theor Appl Genet. 2007 Sep;115(5):601-15

    A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of... Read more

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