Evolution and Domestication Footprints Uncovered from the Genomes of Coix

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.