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Wu Z, Chen H, Pan Y, Feng H, Fang D, Yang J, Wang Y, Yang J, Sahu SK, Liu J, Xing Y, Wang X, Liu M, Luo X, Gao P, Li L, Liu Z, Yang H, Liu X, Xu X, Liu H, Wang E. Genome of Hippophae rhamnoides provides insights into a conserved molecular mechanism in actinorhizal and rhizobial symbioses. New Phytol 2022; 235:276-291. [PMID: 35118662 DOI: 10.1111/nph.18017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Sea buckthorn (Hippophae rhamnoides), a horticulturally multipurpose species in the family Elaeagnaceae, can build associations with Frankia actinomycetes to enable symbiotic nitrogen-fixing. Currently, no high-quality reference genome is available for an actinorhizal plant, which greatly hinders the study of actinorhizal symbiotic nodulation. Here, by combining short-read, long-read and Hi-C sequencing technologies, we generated a chromosome-level reference genome of H. rhamnoides (scaffold N50: 65 Mb, and genome size: 730 Mb) and predicted 30 812 protein-coding genes mainly on 12 pseudochromosomes. Hippophae rhamnoides was found to share a high proportion of symbiotic nodulation genes with Medicago truncatula, implying a shared molecular mechanism between actinorhizal and rhizobial symbioses. Phylogenetic analysis clustered the three paralogous NODULE INCEPTION (NIN) genes of H. rhamnoides with those of other nodulating species, forming the NIN group that most likely evolved from the ancestral NLP group. The genome of H. rhamnoides will help us to decipher the underlying genetic programming of actinorhizal symbiosis, and our high-quality genome and transcriptomic resources will make H. rhamnoides a new excellent model plant for actinorhizal symbiosis research.
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Affiliation(s)
- Zefeng Wu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Hongyun Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Ya Pan
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Huan Feng
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jun Yang
- Shanghai Chenshan Plant Science Research Center (CAS), Shanghai, 210602, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jianling Liu
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Yu'e Xing
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xinyue Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Peng Gao
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Lifeng Li
- Jinzhong Municipal Planning and Natural Resources Bureau, Jinzhong, Shanxi, 030600, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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