Li Ya-Peng, Su Li-Yao, Huang Ting, Liu Hui, Tan Shan-Shan, Deng Yuan-Jie, Wang Ya-Hui, Xiong Ai-Sheng
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
Hortic Res. 2025 Mar 11;12(7):uhaf079. doi: 10.1093/hr/uhaf079. eCollection 2025 Jul.
Pucai () ( L.), within the spp., is a distinctive semiaquatic vegetable. Lignin and chlorophyll are two crucial traits and quality indicators for Pucai. In this study, we assembled a 207.00-Mb high-quality gapless genome of Pucai, telomere-to-telomere (T2T) level with a contig N50 length of 13.73 Mb. The most abundant type of repetitive sequence, comprising 16.98% of the genome, is the long terminal repeat retrotransposons (LTR-RT). A total of 30 telomeres and 15 centromeric regions were predicted. Gene families related to lignin, chlorophyll biosynthesis, and disease resistance were greatly expanded, which played important roles in the adaptation of Pucai to wetlands. The slow evolution of Pucai was indicated by the σ whole-genome duplication (WGD)-associated peaks from different Poales and the low activity of recent LTR-RT in Pucai. Meanwhile, we found a unique WGD event in Typhaceae. A statistical analysis and annotation of genomic variations were conducted in interspecies and intraspecies of . Based on the T2T genome, we constructed lignin and chlorophyll metabolic pathways of Pucai. Subsequently, the candidate structural genes and transcription factors that regulate lignin and chlorophyll biosynthesis were identified. The T2T genomic resources will provide molecular information for lignin and chlorophyll accumulation and help to understand genome evolution in Pucai.
蒲菜（Typha latifolia L.），属于香蒲属植物，是一种独特的半水生蔬菜。木质素和叶绿素是蒲菜的两个关键特性和品质指标。在本研究中，我们组装了一个207.00 Mb的高质量无间隙蒲菜基因组，达到端粒到端粒（T2T）水平，重叠群N50长度为13.73 Mb。最丰富的重复序列类型是长末端重复逆转座子（LTR-RT），占基因组的16.98%。共预测到30个端粒和15个着丝粒区域。与木质素、叶绿素生物合成和抗病性相关的基因家族大幅扩展，这在蒲菜适应湿地环境中发挥了重要作用。不同禾本目的σ全基因组复制（WGD）相关峰值以及蒲菜中近期LTR-RT的低活性表明蒲菜进化缓慢。同时，我们在香蒲科中发现了一个独特的WGD事件。对蒲菜的种间和种内基因组变异进行了统计分析和注释。基于T2T基因组，我们构建了蒲菜的木质素和叶绿素代谢途径。随后，鉴定了调控木质素和叶绿素生物合成的候选结构基因和转录因子。T2T基因组资源将为木质素和叶绿素积累提供分子信息，并有助于了解蒲菜的基因组进化。
