The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)
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DOI：
10.1038/nature12817
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发表时间：
2014-01-23
期刊：
影响因子：
64.8
通讯作者：
Himmelbauer, Heinz
中科院分区：
文献类型：
--
作者：
Dohm, Juliane C.;Minoche, Andre E.;Himmelbauer, Heinz
甜菜（Beta vulgaris ssp. vulgaris）是温带气候的重要作物，其提供了世界每年糖产量的近30%，并且是生物乙醇和动物饲料的来源。该物种属于Caryophylalles目，是二倍体，2n=18条染色体，估计基因组大小为714-758 megabytes（1），与其他真双子叶植物共享古老的基因组三倍体（2）。叶用甜菜自罗马时代就已开始种植，但糖用甜菜是最近才驯化的作物之一。它产生于世纪后期，当时从甜菜和饲料甜菜的杂交中选择了在贮藏根中积累糖的品系（3）。在这里，我们提出了一个参考基因组序列甜菜作为第一个非rosid，非rosid真双子叶植物基因组，推进比较基因组学和系统发育重建。基因组序列包括567兆碱基，其中85%可以分配给染色体。组装体覆盖了大部分的重复序列含量，估计（4）为63%。我们预测了27，421个由转录数据支持的蛋白质编码基因，并根据序列同源性对其进行了注释。系统发育分析提供的证据，分离的Carbellales之前，分裂的pandroid和rosids，并揭示了谱系特异性基因家族的扩展和损失。我们测序菠菜（菠菜），另一种Carbellales物种，并验证功能，分离这个分支从蔷薇科和花梗。基于海甜菜（Beta vulgaris ssp.）maritima;所有甜菜作物的祖先）和四个另外的糖用甜菜加入物。我们在参考基因组中确定了700万个变异位置，以及大面积的低变异区域，这表明了人工选择。甜菜基因组序列能够鉴定影响农艺相关性状的基因，支持分子育种，并最大限度地发挥植物在能源生物技术方面的潜力。
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(1) and shares an ancient genome triplication with other eudicot plants(2). 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(3). 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(4) 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.