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Atanas Pavlov - One of the best experts on this subject based on the ideXlab platform.
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ploidy levels in Beta Vulgaris red beet plant organs and in vitro systems
2010Co-Authors: Jost Weber, Vasil Georgiev, Thomas Bley, Christiane Haas, Atanas PavlovAbstract:The ploidy levels of the cells in different organs (leaves, petioles and roots) of red beet (Beta Vulgaris L.) plants of different ages, as well as of different in vitro systems (transformed hairy roots, calli derived from leaves and rhizogenic calli), were investigated using flow cytometry. Two callus lines with red and yellow phenotypes, derived by mechanical separation of the morphologically heterogeneous rhizogenic callus, were also examined. All investigated samples experienced several cycles of endoreduplication. The older organs exhibited higher levels of polysomaty than the young ones. The highest degree of endoreduplication was found in old petiole tissue and the lowest in the red callus line (cycle values of 1.81 and 0.55, respectively). Interestingly, the callus derived from leaves did not exhibit a 2Cx peak, but was tetraploid, probably due to genetic instability, which may have been caused by prolonged cultivation under in vitro conditions. Red and yellow calli showed significantly lower polysomaty (cycle values of 0.55 and 0.59, respectively) than the primary rhizogenic callus (cycle value of 1.09). The DNA profiles of the two phenotypes differed, possibly reflecting differences in their metabolism.
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improved procedure for nucleus extraction for dna measurements by flow cytometry of red beet Beta Vulgaris l hairy roots
2009Co-Authors: Vasil Georgiev, Jost Weber, Thomas Bley, Atanas PavlovAbstract:Three often cited systems for the extraction of plant nuclei for flow cytometric measurement (CyStain PI, Partec GmbH, Munster, Germany, the method of Arumuganathan and Earle, and LB01 buffer) failed, when applied to the hairy roots of red beet (Beta Vulgaris). By combining these systems and introducing a centrifugation step, the extraction, staining, and analysis of nuclei from this tissue were performed successfully.
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Betalains biosynthesis by Beta Vulgaris l hairy root culture in a temporary immersion cultivation system
2006Co-Authors: Atanas Pavlov, Thomas BleyAbstract:Abstract The process of Betalains biosynthesis by Beta Vulgaris L. hairy root culture in a temporary immersion system was studied. It was established that temporary immersion technique is suitable for the cultivation of hairy roots. The immersion frequency had significant effect on the biomass accumulation and the yields of Betalains. The hairy root culture biosynthesized 18.8 mg g −1 dry biomass (DB) Betalains (9.6 mg g −1 DB Betacyanins and 9.2 mg g −1 DB Betaxanthins) at immersion frequency with 15 min flooding and 60 min stand-by periods. The maximal growth index (16.6) was achieved at 15 min flooding and 75 min stand-by periods. Data on the relationships in the biological system “Nutrient medium– B. Vulgaris L. hairy root culture–Betalains” are presented.
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Radical Scavenging Activity and Stability of Betalains from Beta Vulgaris Hairy Root Culture in Simulated Conditions of Human Gastrointestinal Tract
2005Co-Authors: Atanas Pavlov, Mladenka Ilieva, Petia Kovatcheva, Dimka Tuneva, Thomas BleyAbstract:Stability and radical scavenging activity of Betalains, biosynthesized by Beta Vulgaris hairy root culture were investigated at different pH values, bile salts concentration, as well as at the in vitro conditions of gastrointestinal tract. It was established that pH below 3 and concentrations of the bile salts up to 4% had no great influence on Betalains stability. At the in vitro conditions of gastrointestinal tract Betalains are relatively stable, as their radical scavenging activity decrease from 75% inhibition of 2,2-diphenyl-1-picrylhydrazyl (DPPH•) to about 38%.
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Betalain biosynthesis by red beet Beta Vulgaris l hairy root culture
2005Co-Authors: Atanas Pavlov, Vasil Georgiev, Mladenka IlievaAbstract:The time course of growth and Betalains biosynthesis by Beta Vulgaris L. (cv. Detroit Dark Red) hairy root culture were investigated. It was established that hairy root culture produced 42.2 mg/flasks Betalains (26.2 mg/flasks Betaxanthins and 16.0 Betacyanins) between 6th and 15th days of cultivation. The uptake of sucrose, nitrate and phosphate ions were followed during the cultivation and data on the physiology of the B. Vulgaris hairy root culture are presented.
Richard Reinhardt - One of the best experts on this subject based on the ideXlab platform.
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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract: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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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract:A full genome sequence is presented of sugar beet Beta Vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions. Industrial production of sugar from sugar beet (Beta Vulgaris) began in Europe in the early nineteenth century, and in the intervening 200 years the sugar content of the commonly used cultivars has increased from 8% to 18%. A high-quality reference genome sequence for sugar beet is published in this issue, together with that of the related spinach plant (Spinacia oleracea) and assembled genomes from four additional sugar beet breeding lines. Information held in these genome sequences will be useful for the characterization of genes involved in sugar production and identification of targets for breeding efforts, as well as towards its application as a sustainable energy crop. 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 megabases1 and shares an ancient genome triplication with other eudicot plants2. 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 beet3. 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 estimated4 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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haplotype divergence in Beta Vulgaris and microsynteny with sequenced plant genomes
2009Co-Authors: Juliane C Dohm, Richard Reinhardt, Cornelia Lange, Heinz HimmelbauerAbstract: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 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 11% of either sequence. Of such indels, 68 and 45%, respectively, could be attributed to haplotype-specific integration of transposable elements. We identified novel repeat candidates by comparing the two BAC sequences to a set of genomic sugar beet sequences. Synteny was found with Arabidopsis chromosome 1 (At1), At2 and At4, Medicago chromosome 7, Vitis chromosome 15 and paralogous regions on poplar chromosomes II and XIV.
Juliane C Dohm - One of the best experts on this subject based on the ideXlab platform.
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genomes of the wild beets Beta patula and Beta Vulgaris ssp maritima
2019Co-Authors: Alvaro Rodriguez Del Rio, André E. Minoche, Heinz Himmelbauer, Nikolaus F Zwickl, Anja Friedrich, Susan Liedtke, Thomas Schmidt, Juliane C DohmAbstract: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 were identified, and a display tool for automatic genome-wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research.
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crop wild relative populations of Beta Vulgaris allow direct mapping of agronomically important genes
2017Co-Authors: Gina Capistranogossmann, David Ries, Daniela Holtgräwe, André E. Minoche, S.l.m. Frerichmann, Rosleff T Soerensen, Juliane C Dohm, Thomas Kraft, Irene GonzálezAbstract: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 a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.
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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract: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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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract:A full genome sequence is presented of sugar beet Beta Vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions. Industrial production of sugar from sugar beet (Beta Vulgaris) began in Europe in the early nineteenth century, and in the intervening 200 years the sugar content of the commonly used cultivars has increased from 8% to 18%. A high-quality reference genome sequence for sugar beet is published in this issue, together with that of the related spinach plant (Spinacia oleracea) and assembled genomes from four additional sugar beet breeding lines. Information held in these genome sequences will be useful for the characterization of genes involved in sugar production and identification of targets for breeding efforts, as well as towards its application as a sustainable energy crop. 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 megabases1 and shares an ancient genome triplication with other eudicot plants2. 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 beet3. 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 estimated4 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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haplotype divergence in Beta Vulgaris and microsynteny with sequenced plant genomes
2009Co-Authors: Juliane C Dohm, Richard Reinhardt, Cornelia Lange, Heinz HimmelbauerAbstract: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 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 11% of either sequence. Of such indels, 68 and 45%, respectively, could be attributed to haplotype-specific integration of transposable elements. We identified novel repeat candidates by comparing the two BAC sequences to a set of genomic sugar beet sequences. Synteny was found with Arabidopsis chromosome 1 (At1), At2 and At4, Medicago chromosome 7, Vitis chromosome 15 and paralogous regions on poplar chromosomes II and XIV.
Daniela Holtgräwe - One of the best experts on this subject based on the ideXlab platform.
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crop wild relative populations of Beta Vulgaris allow direct mapping of agronomically important genes
2017Co-Authors: Gina Capistranogossmann, David Ries, Daniela Holtgräwe, André E. Minoche, S.l.m. Frerichmann, Rosleff T Soerensen, Juliane C Dohm, Thomas Kraft, Irene GonzálezAbstract: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 a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.
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Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta Vulgaris)
2014Co-Authors: Ralf Stracke, Daniela Holtgräwe, Thomas Rosleff Sorensen, Jessica Schneider, Boas Pucker, Bernd WeisshaarAbstract:The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Although genome-wide analysis of this gene family has been carried out in some species, the R2R3-MYB genes in Beta Vulgaris ssp. Vulgaris (sugar beet) as the first sequenced member of the order Caryophyllales, have not been analysed heretofore. We present a comprehensive, genome-wide analysis of the MYB genes from Beta Vulgaris ssp. Vulgaris (sugar beet) which is the first species of the order Caryophyllales with a sequenced genome. A total of 70 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Also, organ specific expression patterns were determined from RNA-seq data. The R2R3-MYB genes were functionally categorised which led to the identification of a sugar beet-specific clade with an atypical amino acid composition in the R3 domain, putatively encoding Betalain regulators. The functional classification was verified by experimental confirmation of the prediction that the R2R3-MYB gene Bv_iogq encodes a flavonol regulator. This study provides the first step towards cloning and functional dissection of the role of MYB transcription factor genes in the nutritionally and evolutionarily interesting species B. Vulgaris. In addition, it describes the flavonol regulator BvMYB12, being the first sugar beet R2R3-MYB with an experimentally proven function.
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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract: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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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract:A full genome sequence is presented of sugar beet Beta Vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions. Industrial production of sugar from sugar beet (Beta Vulgaris) began in Europe in the early nineteenth century, and in the intervening 200 years the sugar content of the commonly used cultivars has increased from 8% to 18%. A high-quality reference genome sequence for sugar beet is published in this issue, together with that of the related spinach plant (Spinacia oleracea) and assembled genomes from four additional sugar beet breeding lines. Information held in these genome sequences will be useful for the characterization of genes involved in sugar production and identification of targets for breeding efforts, as well as towards its application as a sustainable energy crop. 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 megabases1 and shares an ancient genome triplication with other eudicot plants2. 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 beet3. 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 estimated4 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.
André E. Minoche - One of the best experts on this subject based on the ideXlab platform.
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genomes of the wild beets Beta patula and Beta Vulgaris ssp maritima
2019Co-Authors: Alvaro Rodriguez Del Rio, André E. Minoche, Heinz Himmelbauer, Nikolaus F Zwickl, Anja Friedrich, Susan Liedtke, Thomas Schmidt, Juliane C DohmAbstract: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 were identified, and a display tool for automatic genome-wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research.
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crop wild relative populations of Beta Vulgaris allow direct mapping of agronomically important genes
2017Co-Authors: Gina Capistranogossmann, David Ries, Daniela Holtgräwe, André E. Minoche, S.l.m. Frerichmann, Rosleff T Soerensen, Juliane C Dohm, Thomas Kraft, Irene GonzálezAbstract: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 a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.
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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract: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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the genome of the recently domesticated crop plant sugar beet Beta Vulgaris
2014Co-Authors: Juliane C Dohm, Daniela Holtgräwe, André E. Minoche, Thomas Rosleff Sorensen, Salvador Capellagutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Ralf Stracke, Richard ReinhardtAbstract:A full genome sequence is presented of sugar beet Beta Vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions. Industrial production of sugar from sugar beet (Beta Vulgaris) began in Europe in the early nineteenth century, and in the intervening 200 years the sugar content of the commonly used cultivars has increased from 8% to 18%. A high-quality reference genome sequence for sugar beet is published in this issue, together with that of the related spinach plant (Spinacia oleracea) and assembled genomes from four additional sugar beet breeding lines. Information held in these genome sequences will be useful for the characterization of genes involved in sugar production and identification of targets for breeding efforts, as well as towards its application as a sustainable energy crop. 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 megabases1 and shares an ancient genome triplication with other eudicot plants2. 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 beet3. 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 estimated4 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.