A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth ( Pontederia crassipes)

Commelinales belongs to the commelinids clade which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is current available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across eight pseudochromosome pairs. With the representative genomes, we reconstructed phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having eight chromosomes but not five as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using nine water hyacinth lines from three continents (South America, Asia and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, and provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commilinids species and offer novel insights into their phylogeny.