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

Abstract

Pucai () (Typha angustifolia L.), within the Typha 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 Ks 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 Typha. 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.

Figure 1

Phenotypes and growing environment of Pucai. (A): Phenotypes of Pucai. (B): Growing environment of Pucai. (C): Pseudostem of Pucai.

Figure 2

T2T complete reference genome of Pucai. (A): Hi-C interaction matrix based on the TaT2T assembly. (B): Circus display of significant characteristics of the TaT2T genome. (a), chromosome names and sizes, with centromere (red) and telomere (black) positions marked (b), density of HC genes (c), distribution of GC content (d), density of DNA TE (e), density of Copia (f), density of Gypsy (g), density of satellite repeats (h), links between syntenic genes. (C): LAI of the TaT2T genome. (D): LTR-RT insertion bursts of Pucai compared to those in O. sativa, S. stoloniferum, and A. comosus. (E): Insertion bursts of Gypsy and Copia of Pucai.

Figure 3

Comparative genomics of gene families of Pucai. (A): Number of shared orthologous gene families among 13 genomes. (B): KEGG enrichment of Pucai-unique gene families. (C): Estimation of divergence time and expanded/contracted gene families. (D): KEGG enrichment of expanded gene families of Pucai. (E): Functional annotation for the expanded gene families in Pucai. The left panel illustrates the sizes of gene families across 13 species, while the right panel presents the functional annotations associated with these gene families.

Figure 4

WGDs in Pucai. (A): Ks distribution. (B): Dot plots of paralogues and orthologues. (C): Ks values of gene pairs originating from WGD genes. (D): GO enrichment analyses of WGD genes.

Figure 5

Huge number of variations among Typha genomes. (A): Syntenic analyses among the T. latifolia, T. angustifolia V1, and TaT2T genomes. (B): Statistics of inter- and intraspecies variations. (C): Annotation of interspecies SNPs and InDel.

Figure 6

Lignin and chlorophyll content and biosynthesis of Pucai. (A): Three sampling sections of the Pucai pseudostem. (B): Lignin content. (C): Chlorophyll content. (D): Cross-section after treatment with phloroglucin-HCL and fluorescence micrographs. (E): Expression profiles of genes involved in lignin biosynthesis. (F): Expression profiles of genes involved in chlorophyll biosynthesis.

Figure 7

Potential key genes involved in lignin and chlorophyll biosynthesis. (A): Venn map and heat map of key genes involved in lignin biosynthesis. (B): Venn map and heat map of key genes in chlorophyll biosynthesis. (C): Network diagram of key genes involved in lignin biosynthesis. (D): Network diagram of key genes involved in chlorophyll biosynthesis.

Figure 8

TaT2T genome and transcriptome of Pucai promote molecular breeding on Pucai