Wang Jia-Le, Zhang Wen-Da, Yang Xiao-Dong, Zhao Pu-Guang, Wang Xiang-Yu, Zhao Shu-Ying, Chen Ling-Yun
School of Environment and Ecology, Jiangsu Open University, Nanjing 210036, China.
School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
DNA Res. 2025 Mar 1;32(2). doi: 10.1093/dnares/dsaf002.
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.
梭鱼草是一种原产于美洲的水生观赏植物，但已广泛分布于南亚、澳大利亚和欧洲。其快速适应和传播背后的遗传机制尚未得到充分了解。为了了解其快速适应的机制，本研究组装了首个梭鱼草染色体水平的基因组。该基因组组装大小为527.5 Mb，锚定在8条假染色体上，支架N50为48 Mb，包含29,389个蛋白质编码基因。进一步分析表明，梭鱼草经历了3次全基因组复制（WGD）事件。这些WGD与基因家族扩张以及抗性基因类似物和转录因子数量增加有关。正选择分析表明，串联重复（TD）和近端重复产生的基因更有可能经历正选择，并且在植物防御和抗病性方面富集。这些结果表明，WGD、TD和正选择增强了梭鱼草的环境适应性。此外，我们发现F3'5'H、DFR、ANS和UFGT的下调可能导致梭鱼草花色从紫色变为白色。这里的首个梭鱼草染色体水平基因组为研究该物种的快速适应和花色变异提供了宝贵的基因组资源。
