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

机译：最近驯化的农作物甜菜（Beta vulgaris）的基因组

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摘要

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 In = 18 chromosomes, has an estimated genome size of 714-758 mega-bases 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. maritimn; 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 agronomical!) relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.%用甜菜(Beta vulgaris)制糖的工业化生产是19世纪早期在欧洲开始的，在此后的200年间常用栽培品种的糖含霣从8%增加到了18%。本期WNature发表了甜菜的一个高质量参考基因组序列，同时还发表了与其相关的菠菜（Spinacia oleracea)的基因组序列以及另外四种甜菜繁殖系的综合基因组。这些基因组序列中所含信息对于在糖生成中所涉及基因的定性、对于育种工作目标的确定、以及对于它作为一种可持续性能源作物的应用都将会是有用的。
机译：甜菜（Beta vulgaris ssp。vulgaris）是温带气候的重要农作物，占全球年糖产量的近30％，是生物乙醇和动物饲料的来源。该物种属于石竹科，是具有In = 18个染色体的二倍体，估计的基因组大小为714-758兆碱基，并且与其他双子叶植物共享古老的基因组三倍体。自罗马时代以来就开始种植绿叶甜菜，但是甜菜是最近驯化的农作物之一。它起源于十八世纪末，当时从用甜菜和饲料甜菜制成的杂交品种中选出了在贮藏根部积累糖分的品系。在这里，我们提出了甜菜的参考基因组序列，作为第一个非rosid，non-asterid eudicot基因组，推进了比较基因组学和系统发育重建。基因组序列包含567个兆碱基，其中85％可分配给染色体。该程序集覆盖了重复序列内容的很大一部分，估计为63％。我们预测了转录数据支持的27,421个蛋白质编码基因，并根据序列同源性对其进行了注释。系统发育分析为核糖体在类固醇和rosids分裂之前的分离提供了证据，并揭示了谱系特异性基因家族的扩展和损失。我们对菠菜（菠菜（Spinacia oleracea））（另一种石竹科物种）进行了测序，并验证了将这种进化枝与玫瑰红和紫杉醇分开的功能。基于海甜菜（Bet vulgaris ssp。maritimn；所有甜菜作物的祖先）的基因组序列和另外四个甜菜种质进行了种内基因组变异分析。我们在参考基因组中发现了700万个变异位置，并且还发现了低变异性的大区域，这表明是人工选择。甜菜基因组序列能够识别影响农艺学相关性状的基因，支持分子育种，并最大限度地利用植物在能源生物技术中的潜力。％用甜菜（Beta vulgaris）制糖的工业化生产是19世纪早期在欧洲开始的，在此后的200年间常用栽培品种的糖含霣从8％增加到了18％。本期WNature发表了甜菜的一个替代参考基因组序列，同时还发表了与此相关的菠菜（Spinacia oleracea）的基因组序列以及这些基因组序列中所含信息关于在糖生成中所涉及到基因的定性，关于育种工作目标的确定，以及针对它作为一种可持续性能源作物的应用都将会是有用的。

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  • 来源
    《Nature》 |2014年第7484期|546-549A3|共5页
  • 作者

    Juliane C. Dohm; Andre E. Minoche; Daniela Holtgrawe; Salvador Capella-Gutierrez; Falk Zakrzewski; Hakim Tafer; Oliver Rupp; Thomas Rosleff Sorensen; Ralf Stracke; Richard Reinhardt; Alexander Goesmann; Thomas Kraft; Britta Schulz; Peter F. Stadler; Thomas Schmidt; Toni Gabaldon; Hans Lehrach; Bernd Weisshaar; Heinz Himmelbauer;

  • 作者单位

    Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany,Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88,08003 Barcelona, Spain;

    Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany,Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88,08003 Barcelona, Spain;

    Bielefeld University, CeBiTec and Department of Biology, Universitaetsstrasse 25,33615 Bielefeld, Germany;

    Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain,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, Haertelstrasse 16-18, 04107 Leipzig, Germany;

    Bielefeld University, CeBiTec and Department of Biology, Universitaetsstrasse 25,33615 Bielefeld, Germany;

    Bielefeld University, CeBiTec and Department of Biology, Universitaetsstrasse 25,33615 Bielefeld, Germany;

    Bielefeld University, CeBiTec and Department of Biology, Universitaetsstrasse 25,33615 Bielefeld, Germany;

    Max Planck Genome Centre Cologne, Carl-von- Linne-Weg 10, 50829 Koeln, Germany;

    Max Planck Genome Centre Cologne, Carl-von- Linne-Weg 10, 50829 Koeln, Germany;

    Syngenta, Box 302,26123 Landskrona, Sweden;

    KWSSAATAG, Grimsehlstrasse 31,37574 Einbeck, Germany;

    University of Leipzig, Department of Computer Science, Haertelstrasse 16-18, 04107 Leipzig, Germany;

    TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany;

    Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88,08003 Barcelona, Spain,Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany;

    Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany;

    Bielefeld University, CeBiTec and Department of Biology, Universitaetsstrasse 25,33615 Bielefeld, Germany;

    Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany,Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88,08003 Barcelona, Spain;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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