Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis
Abstract Phragmites australis is a globally distributed grass species (Poaceae) recognized for its vast biomass and exceptional environmental adaptability, making it an ideal model for studying wetland ecosystems and plant stress resilience. However, genomic resources for this species have been limi...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-07532-y |
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| author | Jipeng Cui Rui Wang Ruoqing Gu Minghui Chen Ziyao Wang Li Li Jianming Hong Suxia Cui |
| author_facet | Jipeng Cui Rui Wang Ruoqing Gu Minghui Chen Ziyao Wang Li Li Jianming Hong Suxia Cui |
| author_sort | Jipeng Cui |
| collection | DOAJ |
| description | Abstract Phragmites australis is a globally distributed grass species (Poaceae) recognized for its vast biomass and exceptional environmental adaptability, making it an ideal model for studying wetland ecosystems and plant stress resilience. However, genomic resources for this species have been limited. In this study, we assembled a chromosome-level reference genome of P. australis containing one B chromosome. An explosion of LTR-RTs, centered on the Copia family, occurred during the late Pleistocene, driving the expansion of P. australis genome size and subgenomic differentiation. Comparative genomic analysis showed that P. australis underwent two whole gene duplication events, was segregated from Cleistogenes songorica at 34.6 Mya, and that 41.26% of the gene families underwent expansion. Based on multi-tissue transcriptomic data, we identified structural genes in the biosynthetic pathway of pharmacologically active Phragmitis rhizoma polysaccharides with essential roles in rhizome development. This study deepens our understanding of Arundinoideae evolution, genome dynamics, and the genetic basis of key traits, providing essential data and a genetic foundation for wetland restoration, bioenergy development, and plant stress. |
| format | Article |
| id | doaj-art-41e1e797e4844cc9882851925e463257 |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-41e1e797e4844cc9882851925e4632572025-01-19T12:35:14ZengNature PortfolioCommunications Biology2399-36422025-01-018112010.1038/s42003-025-07532-yTelomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesisJipeng Cui0Rui Wang1Ruoqing Gu2Minghui Chen3Ziyao Wang4Li Li5Jianming Hong6Suxia Cui7College of Life Sciences, Capital Normal UniversityCollege of Life Sciences, Capital Normal UniversityCollege of Life Sciences, Capital Normal UniversityCollege of Life Sciences, Capital Normal UniversityCollege of Life Sciences, Capital Normal UniversityCollege of Life Sciences, Capital Normal UniversityCollege of Life Sciences, Capital Normal UniversityCollege of Life Sciences, Capital Normal UniversityAbstract Phragmites australis is a globally distributed grass species (Poaceae) recognized for its vast biomass and exceptional environmental adaptability, making it an ideal model for studying wetland ecosystems and plant stress resilience. However, genomic resources for this species have been limited. In this study, we assembled a chromosome-level reference genome of P. australis containing one B chromosome. An explosion of LTR-RTs, centered on the Copia family, occurred during the late Pleistocene, driving the expansion of P. australis genome size and subgenomic differentiation. Comparative genomic analysis showed that P. australis underwent two whole gene duplication events, was segregated from Cleistogenes songorica at 34.6 Mya, and that 41.26% of the gene families underwent expansion. Based on multi-tissue transcriptomic data, we identified structural genes in the biosynthetic pathway of pharmacologically active Phragmitis rhizoma polysaccharides with essential roles in rhizome development. This study deepens our understanding of Arundinoideae evolution, genome dynamics, and the genetic basis of key traits, providing essential data and a genetic foundation for wetland restoration, bioenergy development, and plant stress.https://doi.org/10.1038/s42003-025-07532-y |
| spellingShingle | Jipeng Cui Rui Wang Ruoqing Gu Minghui Chen Ziyao Wang Li Li Jianming Hong Suxia Cui Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis Communications Biology |
| title | Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis |
| title_full | Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis |
| title_fullStr | Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis |
| title_full_unstemmed | Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis |
| title_short | Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis |
| title_sort | telomere to telomere phragmites australis reference genome assembly with a b chromosome provides insights into its evolution and polysaccharide biosynthesis |
| url | https://doi.org/10.1038/s42003-025-07532-y |
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