Coix lacryma-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 ∼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 (∼2.3-fold) due mainly to the activity of transposable elements. Phylogenetic analysis revealed that coix diverged with sorghum ∼10.41 million years ago, which was ∼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.

Ze豆与玉米和高粱密切相关，是亚洲重要的粮食和药用作物。然而，没有报道该物种的参考基因组，并且其在雄性菊科中的确切系统发育仍未解析。在这里，我们生成了co的高质量基因组组装体，其中包含约1.73 Gb与44 485个预测的蛋白质编码基因。我们发现co是一种典型的二倍体植物，与高粱具有整体一对一的同线关系。尽管由于可转座因子的活性，其基因组急剧扩增（约2.3倍），但仍具有较高的基因组效率。系统发育分析表明，co与高粱的发散时间约为1041万年前，比高粱和玉米的发散时间晚了149万年。对另外27种co的重新测序表明，它们可以明确地分为野生亲缘种和品种，并表明co经历了强大的遗传瓶颈，即使许多性状仍未驯化，也导致驯化过程中遗传多样性丧失了大约一半。 。我们的数据不仅提供了对Andropogoneae世系的新颖的比较基因组学和进化见解，而且还提供了一种重要资源，将大大有益于该重要作物的分子育种。