Nature2014-06-26 4:58 PM

甜菜的参照基因组序列 The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

论文摘要 

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量从8%增加到了18%。本期Nature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。

Abstract 

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 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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