Chromosome-level genome assembly of Pontederia cordata L. provides insights into its rapid adaptation and variation of flower colours.

Pontederia cordata L. is an aquatic ornamental plant native to the Americas but has been widely distributed in South Asia, Australia, and Europe. The genetic mechanisms behind its rapid adaptation and spread have not yet been well understood. To understand the mechanisms for its rapid adaptation, this study assembled the first chromosome-level genome of P. cordata. The genome assembly, which spans 527.5 Mb, is anchored on 8 pseudochromosomes with a scaffold N50 of 48 Mb and encompasses 29,389 protein-coding genes. Further analyses revealed that P. cordata had experienced 3 whole-genome duplications (WGDs) events. These WGDs are associated with gene family expansion and increased numbers of resistance gene analogs and transcription factors. Positive selection analysis indicated that genes derived from tandem duplication (TD) and proximal duplication were more likely to undergo positive selection, and were enriched in plant defense and disease resistance. These results implied that WGDs, TD, and positive selection enhanced the environmental adaptability of P. cordata. In addition, we found that down-regulation of F3'5'H, DFR, ANS, and UFGT likely caused the flower colour variation for P. cordata from violet to white. The first chromosome-level genome of P. cordata here provides a valuable genomic resource for investigating the rapid adaptation and flower colour variation of the species.