Repetitive sequence analysis and karyotyping reveal different genome evolution and speciation of diploid and tetraploid Tripsacum dactyloides

In the subtribe Maydeae, Tripsacum and Zea are closely related genera. Tripsacum is a horticultural crop widely used as pasture forage. Previous studies suggested that Tripsacum might play an important role in maize origin and evolution. However, our understanding of the genomics and the evolution of Tripsacum remains limited. In this study, two diploids,T. dactyloides var. meridionale(2n = 36, MR) and T. dactyloides(2n = 36, DD), and one tetraploid,T. dactyloides(2n = 72, DL) were sequenced by low-coverage genome sequencing followed by graph-based cluster analysis. The results showed that 63.23%, 59.20%, and 61.57% of the respective genome of MR, DD, and DL were repetitive DNA sequence. The proportions of different repetitive sequences varied greatly among the three species. Fluorescence in situ hybridization(FISH) analysis of mitotic metaphase chromosomes with satellite repeats as the probes showed that the FISH signal patterns of DL were more similar to that of DD than to that of MR. Comparative analysis of the repeats also showed that DL shared more common repeat families with DD than with MR. Phylogenetic analysis of internal transcribed spacer region sequences further supported the evolutionary relationship among the three species. Repetitive sequences comparison showed that Tripsacum shared more repeat families with Zea than with Coix and Sorghum. Our study sheds new light on the genomics of Tripsacum and differential speciation in the Poaceae family.

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 44485 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.