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

作者：Yujie Huang, Longbiao Guo, Lingjuan Xie, Nianmin Shang, Dongya Wu, Chuyu Ye, Eduardo Carlos Rüdell, Kazunori Okada, Qian‐Hao Zhu, Beng-Kah Song, Daguang Cai, Aldo Merotto, Lianyang Bai, Longjiang Fan · 发表于：GigaScience · 年份：2024 · DOI：10.1093/gigascience/giae006 · 被引用次数：12 · 研究领域：Biological Control of Invasive Species、Plant tissue culture and regeneration、Weed Control and Herbicide Applications

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 currently 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 8 pseudochromosome pairs. With the representative genomes, we reconstructed a 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 8 chromosomes but not 5 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 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here ...