Evolution and Domestication Footprints Uncovered from the Genomes of Coix
Evolution and Domestication Footprints Uncovered from the Genomes of Coix
复制标题
从薏苡仁基因组中发现的进化和驯化足迹
DOI：
10.1016/j.molp.2019.11.009
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发表时间：
2020-02-03
期刊：
影响因子：
27.5
通讯作者：
Jin, Weiwei
中科院分区：
文献类型：
--
作者：
Liu, Hongbing;Shi, Junpeng;Jin, Weiwei
薏苡（Coixlactyma-jobi）是与玉米、高粱等近缘的植物，是亚洲重要的粮、药兼用作物。然而，该物种的参考基因组尚未报道，其在仙女草族内的确切的同源性仍然没有解决。在这里，我们产生了一个高质量的基因组组装薏苡包含类似于1.73 Gb与44 485预测的蛋白质编码基因。我们发现薏苡是一个典型的二倍体植物与整体1对1同线的关系与Sorpus基因组，尽管其激烈的基因组扩增（类似2.3倍），主要是由于转座因子的活动。系统发育分析显示，薏苡与高粱的分化时间约为1041万年前，比高粱与玉米的分化时间晚149万年。对另外27份薏苡种质的重测序表明，它们可以明确地分为野生近缘种和栽培种，并表明薏苡经历了一个强大的遗传瓶颈，导致驯化过程中约一半的遗传多样性丧失，尽管许多性状仍未驯化。我们的数据不仅提供了新的比较基因组学和进化的见解Andropogoneae谱系，但也是一个重要的资源，将大大有利于分子育种的这一重要作物。
Coix lactyma-jobi, a plant species closely related to Zea and Sorghum, is an important food and medicinal crop in Asia. However, no reference genome of this species has been reported, and its exact phylogeny within the Andropogoneae remains unresolved. Here, we generated a high-quality genome assembly of coix comprising similar to 1.73 Gb with 44 485 predicted protein-coding genes. We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome, despite its drastic genome expansion (similar to 2.3-fold) due mainly to the activity of transposable elements. Phylogenetic analysis revealed that coix diverged with sorghum similar to 10.41 million years ago, which was similar to 1.49 million years later than the divergence between sorghum and maize. Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars, and suggested that coix experienced a strong genetic bottleneck, resulting in the loss of about half of the genetic diversity during domestication, even though many traits have remained undomesticated. Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage, but also an important resource that will greatly benefit molecular breeding of this important crop.