The giant genome of lily provides insights into the hybridization of cultivated lilies
Abstract Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of their genomic information has impeded evolutionary studies and genome-based breeding efforts. Here, we present reference genomes for Lilium sargentiae (lily, 35.66 Gb) and...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55545-8 |
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| author | Yuwei Liang Qiang Gao Fan Li Yunpeng Du Jian Wu Wenqiang Pan Shaokun Wang Xiuhai Zhang Mingfang Zhang Xiaoming Song Linlin Zhong Fan Zhang Yan Li Zhiwei Wang Danqing Li Qing Duan Shenchong Li Chunlian Jin Peihua Zhang Yang Gu Zhong-Hua Chen Klaus F. X. Mayer Xiaofan Zhou Jihua Wang Liangsheng Zhang |
| author_facet | Yuwei Liang Qiang Gao Fan Li Yunpeng Du Jian Wu Wenqiang Pan Shaokun Wang Xiuhai Zhang Mingfang Zhang Xiaoming Song Linlin Zhong Fan Zhang Yan Li Zhiwei Wang Danqing Li Qing Duan Shenchong Li Chunlian Jin Peihua Zhang Yang Gu Zhong-Hua Chen Klaus F. X. Mayer Xiaofan Zhou Jihua Wang Liangsheng Zhang |
| author_sort | Yuwei Liang |
| collection | DOAJ |
| description | Abstract Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of their genomic information has impeded evolutionary studies and genome-based breeding efforts. Here, we present reference genomes for Lilium sargentiae (lily, 35.66 Gb) and Gloriosa superba (flame lily, 5.09 Gb). The giant lily genome is shaped by recent long terminal repeat retroelements. Phylogenetic analysis reveals diverse, independent origins of lily cultivars. Gene families involved in sucrose and starch metabolism are significantly expanded in the lily genome. Key homologs of XTH22, SOC1, and AP1/FUL-like genes regulate the development, bud growth transition, and floral bud growth transition of lily bulbs. Colchicine biosynthetic gene clusters are identified in G. superba but are absent in L. sargentiae, highlighting independent colchicine evolution in Colchicaceae. These genomic insights enhance understanding of Liliales evolution, providing a foundation for future breeding and molecular research. |
| format | Article |
| id | doaj-art-7031ba0f7d434c74b2aa298e83b993d7 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-7031ba0f7d434c74b2aa298e83b993d72025-01-05T12:37:47ZengNature PortfolioNature Communications2041-17232025-01-0116111610.1038/s41467-024-55545-8The giant genome of lily provides insights into the hybridization of cultivated liliesYuwei Liang0Qiang Gao1Fan Li2Yunpeng Du3Jian Wu4Wenqiang Pan5Shaokun Wang6Xiuhai Zhang7Mingfang Zhang8Xiaoming Song9Linlin Zhong10Fan Zhang11Yan Li12Zhiwei Wang13Danqing Li14Qing Duan15Shenchong Li16Chunlian Jin17Peihua Zhang18Yang Gu19Zhong-Hua Chen20Klaus F. X. Mayer21Xiaofan Zhou22Jihua Wang23Liangsheng Zhang24Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang UniversityZhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang UniversityYunnan Seed LaboratoryInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry SciencesBeijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, Agricultural UniversityInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry SciencesBeijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, Agricultural UniversityInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry SciencesInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry SciencesCenter for Genomics and Bio-computing, College of Life Sciences, North China University of Science and TechnologyNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural UniversityNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural UniversityQi BiodesignQi BiodesignDepartment of Landscape Architecture, School of Civil Engineering and Architecture, Zhejiang Sci-Tech UniversityYunnan Seed LaboratoryYunnan Seed LaboratoryYunnan Seed LaboratoryYunnan Seed LaboratoryCollege of Food Science and Technology, Yunnan Agricultural UniversitySchool of Science, Western Sydney UniversityPlant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Center MunichState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural UniversityYunnan Seed LaboratoryZhejiang Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang UniversityAbstract Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of their genomic information has impeded evolutionary studies and genome-based breeding efforts. Here, we present reference genomes for Lilium sargentiae (lily, 35.66 Gb) and Gloriosa superba (flame lily, 5.09 Gb). The giant lily genome is shaped by recent long terminal repeat retroelements. Phylogenetic analysis reveals diverse, independent origins of lily cultivars. Gene families involved in sucrose and starch metabolism are significantly expanded in the lily genome. Key homologs of XTH22, SOC1, and AP1/FUL-like genes regulate the development, bud growth transition, and floral bud growth transition of lily bulbs. Colchicine biosynthetic gene clusters are identified in G. superba but are absent in L. sargentiae, highlighting independent colchicine evolution in Colchicaceae. These genomic insights enhance understanding of Liliales evolution, providing a foundation for future breeding and molecular research.https://doi.org/10.1038/s41467-024-55545-8 |
| spellingShingle | Yuwei Liang Qiang Gao Fan Li Yunpeng Du Jian Wu Wenqiang Pan Shaokun Wang Xiuhai Zhang Mingfang Zhang Xiaoming Song Linlin Zhong Fan Zhang Yan Li Zhiwei Wang Danqing Li Qing Duan Shenchong Li Chunlian Jin Peihua Zhang Yang Gu Zhong-Hua Chen Klaus F. X. Mayer Xiaofan Zhou Jihua Wang Liangsheng Zhang The giant genome of lily provides insights into the hybridization of cultivated lilies Nature Communications |
| title | The giant genome of lily provides insights into the hybridization of cultivated lilies |
| title_full | The giant genome of lily provides insights into the hybridization of cultivated lilies |
| title_fullStr | The giant genome of lily provides insights into the hybridization of cultivated lilies |
| title_full_unstemmed | The giant genome of lily provides insights into the hybridization of cultivated lilies |
| title_short | The giant genome of lily provides insights into the hybridization of cultivated lilies |
| title_sort | giant genome of lily provides insights into the hybridization of cultivated lilies |
| url | https://doi.org/10.1038/s41467-024-55545-8 |
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