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.

鸭跖草目（Commelinales）隶属于鸭跖草类分支（commelinids clade），该分支同时包含禾本目（Poales）——禾本目囊括了水稻、小麦、玉米等最为重要的单子叶植物类群。目前尚无公开的鸭跖草目参考基因组。凤眼蓝（Water hyacinth，学名Pontederia crassipes 或 Eichhornia crassipes）作为鸭跖草目成员，虽是兼具观赏与药用价值的栽培植物，却也是极具破坏性的水生恶性杂草之一。本研究报道了一份四倍体凤眼蓝的染色体级参考基因组，其组装总长度达1.22 Gb，覆盖预估基因组大小的95%以上，序列被挂载至8对假染色体（pseudochromosome）。依托该代表性基因组，我们重构了鸭跖草类的系统发育关系，结果支持姜目（Zingiberales）与鸭跖草目为棕榈目（Arecales）的姊妹群，为该类群间长期存在争议的目级亲缘关系提供了新的解析依据。本研究同时重构了鸭跖草类分支的祖先核型，证实鸭跖草类的祖先基因组拥有8条染色体，而非此前报道的5条。基因家族分析显示，凤眼蓝多倍化过程中抗病基因发生了收缩，这大概率与其作为恶性杂草的适应性演化需求相关。对来自南美洲、亚洲、欧洲三大洲的9份凤眼蓝材料开展遗传多样性分析，结果显示其核基因组亲缘关系极近，叶绿体基因组几乎完全一致，同时为凤眼蓝的全球扩散路径提供了重要线索。本研究报道的凤眼蓝基因组资源，填补了鸭跖草类物种研究中关键的缺失环节，为该类群的系统演化研究提供了全新的视角。