Rosaceae phylogenomic studies provide insights into the evolution of new genes
Rosa banksiae, known as Lady Banks' rose, is a perennial ornamental crop and a versatile herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled a HiFi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R. banksiae genome with a...
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KeAi Communications Co., Ltd.
2025-01-01
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| Series: | Horticultural Plant Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468014124000694 |
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| author | Lan Jiang Xiaoxu Li Kun Lyu Han Wang Zhiyuan Li Wang Qi Lin Zhang Yunpeng Cao |
| author_facet | Lan Jiang Xiaoxu Li Kun Lyu Han Wang Zhiyuan Li Wang Qi Lin Zhang Yunpeng Cao |
| author_sort | Lan Jiang |
| collection | DOAJ |
| description | Rosa banksiae, known as Lady Banks' rose, is a perennial ornamental crop and a versatile herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled a HiFi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R. banksiae genome with a scaffold N50 = 63.90 Mb. The genome of R. banksiae exhibited no lineage-specific whole-genome duplication compared with other Rosaceae. The phylogenomic analysis of 13 Rosaceae and Arabidopsis through a comparative genomics study showed that numerous gene families were lineage-specific both before and after the diversification of Rosaceae. Some of these genes are candidates for new genes that have evolved from parental genes through fusion events. Fusion genes are divided into three types: Type-I and Type-II genes contain two parental genes that are generated by duplication, distributed in the same and different regions of the genome, respectively; and Type-III can only be detected in one parental gene. Here, Type-I genes are found to have more relaxed selection pressure and lower Ks values than Type-II, indicating that these newly evolved Type-I genes may play important roles in driving phenotypic evolution. Functional analysis exhibited that newly formed fusion genes can regulate the phenotype traits of plant growth and development, suggesting the functional significance of these genes. This study identifies new fusion genes that could be responsible for phenotype evolution and provides information on the evolutionary history of recently diverged species in the Rosa genus. Our data represents the major progress in understanding the new fusion genes evolution pattern of Rosaceae and provides an invaluable resource for phylogenomic studies in plants. |
| format | Article |
| id | doaj-art-8b891c4526f145a58e10ab56c5eae2d4 |
| institution | DOAJ |
| issn | 2468-0141 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Horticultural Plant Journal |
| spelling | doaj-art-8b891c4526f145a58e10ab56c5eae2d42025-08-20T02:40:06ZengKeAi Communications Co., Ltd.Horticultural Plant Journal2468-01412025-01-0111138940510.1016/j.hpj.2024.02.002Rosaceae phylogenomic studies provide insights into the evolution of new genesLan Jiang0Xiaoxu Li1Kun Lyu2Han Wang3Zhiyuan Li4Wang Qi5Lin Zhang6Yunpeng Cao7Anhui Province Key Laboratory of Non-coding RNA Basic and Clinical Transformation (Wannan Medical College), Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241000, ChinaBeijing Life Science Academy, Beijing 102209, ChinaAnhui Province Key Laboratory of Non-coding RNA Basic and Clinical Transformation (Wannan Medical College), Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241000, ChinaSchool of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, ChinaKey Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shangdong 266000, ChinaKey Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shangdong 266000, ChinaSchool of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei 430074, China; Corresponding author.Rosa banksiae, known as Lady Banks' rose, is a perennial ornamental crop and a versatile herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled a HiFi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R. banksiae genome with a scaffold N50 = 63.90 Mb. The genome of R. banksiae exhibited no lineage-specific whole-genome duplication compared with other Rosaceae. The phylogenomic analysis of 13 Rosaceae and Arabidopsis through a comparative genomics study showed that numerous gene families were lineage-specific both before and after the diversification of Rosaceae. Some of these genes are candidates for new genes that have evolved from parental genes through fusion events. Fusion genes are divided into three types: Type-I and Type-II genes contain two parental genes that are generated by duplication, distributed in the same and different regions of the genome, respectively; and Type-III can only be detected in one parental gene. Here, Type-I genes are found to have more relaxed selection pressure and lower Ks values than Type-II, indicating that these newly evolved Type-I genes may play important roles in driving phenotypic evolution. Functional analysis exhibited that newly formed fusion genes can regulate the phenotype traits of plant growth and development, suggesting the functional significance of these genes. This study identifies new fusion genes that could be responsible for phenotype evolution and provides information on the evolutionary history of recently diverged species in the Rosa genus. Our data represents the major progress in understanding the new fusion genes evolution pattern of Rosaceae and provides an invaluable resource for phylogenomic studies in plants.http://www.sciencedirect.com/science/article/pii/S2468014124000694Rosa banksiaeGap-free genomeRosaceaePhenotypeEvolutionary patterns |
| spellingShingle | Lan Jiang Xiaoxu Li Kun Lyu Han Wang Zhiyuan Li Wang Qi Lin Zhang Yunpeng Cao Rosaceae phylogenomic studies provide insights into the evolution of new genes Horticultural Plant Journal Rosa banksiae Gap-free genome Rosaceae Phenotype Evolutionary patterns |
| title | Rosaceae phylogenomic studies provide insights into the evolution of new genes |
| title_full | Rosaceae phylogenomic studies provide insights into the evolution of new genes |
| title_fullStr | Rosaceae phylogenomic studies provide insights into the evolution of new genes |
| title_full_unstemmed | Rosaceae phylogenomic studies provide insights into the evolution of new genes |
| title_short | Rosaceae phylogenomic studies provide insights into the evolution of new genes |
| title_sort | rosaceae phylogenomic studies provide insights into the evolution of new genes |
| topic | Rosa banksiae Gap-free genome Rosaceae Phenotype Evolutionary patterns |
| url | http://www.sciencedirect.com/science/article/pii/S2468014124000694 |
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