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

Abstract

Pucai (蒲菜) (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.

Acknowledgements

This article was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions Project (PAPD), Coordinated Extension of Major Agricultural Technologies Program of Jiangsu (2022-ZYXT-01-3). The study was supported by the Bioinformatics Center of Nanjing Agricultural University. Thanks to Associate Professor Guang-Long Wang from Huaiyin Institute of Technology and Associate Professor Ling-Yun Chen from China Pharmaceutical University for the assistance.

Author contributions

A.S.X. initiated and designed the research. Y.P.L. and L.Y.S. performed the experiments. Y.P.L., L.Y.S., T.H., H.L., S.S.T., Y.J.D., and Y.H.W. analyzed the data. A.S.X. contributed reagents/materials/analysis tools. Y.P.L. wrote the paper. A.S.X. and Y.P.L. revised the paper. All authors read and approved of the final manuscript.

Data availability

The assembled Pucai genome can be downloaded from the NCBI (https://www.ncbi.nlm.nih.gov/) database with the BioProject accession number PRJNA1221093. The transcriptome sequencing data generated in this study have been deposited in the NCBI Sequence Read Archive (SRA) database under accession number PRJNA1221065. The date is available in the figures of the article and its supplementary materials.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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