Journal
MOLECULAR PLANT
Volume 13, Issue 2, Pages 295-308Publisher
CELL PRESS
DOI: 10.1016/j.molp.2019.11.009
Keywords
Coix lacryma-jobi L.; genome; comparative genomics; domestication
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Funding
- National Key Research and Development Program of China [2016YFD0101003]
- National Natural Science Foundation of China [91735305, 91435206, 91635303-3, 31701430, 31421005]
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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.
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