The telomere-to-telomere genome of Pucai () ( <i>Typha angustifolia</i> L.): a distinctive semiaquatic vegetable with lignin and chlorophyll as quality characteristics

Pucai () (<i>Typha angustifolia</i> L.), within the <i>Typha</i> 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 <i>Ks</i> 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 <i>Typha</i>. 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.