Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature
Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-11-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.773090/full |
| _version_ | 1818997636671209472 |
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| author | Lian-Ying Shen Hang Luo Xiao-Ling Wang Xue-Meng Wang Xiao-Jing Qiu Hui Liu Shan-Shan Zhou Kai-Hua Jia Shuai Nie Yu-Tao Bao Ren-Gang Zhang Quan-Zheng Yun Ying-Hui Chai Jin-Ying Lu Yu Li Shu-Wei Zhao Jian-Feng Mao Shan-Gang Jia Yong-Min Mao |
| author_facet | Lian-Ying Shen Hang Luo Xiao-Ling Wang Xue-Meng Wang Xiao-Jing Qiu Hui Liu Shan-Shan Zhou Kai-Hua Jia Shuai Nie Yu-Tao Bao Ren-Gang Zhang Quan-Zheng Yun Ying-Hui Chai Jin-Ying Lu Yu Li Shu-Wei Zhao Jian-Feng Mao Shan-Gang Jia Yong-Min Mao |
| author_sort | Lian-Ying Shen |
| collection | DOAJ |
| description | Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future. |
| first_indexed | 2024-12-20T21:48:47Z |
| format | Article |
| id | doaj.art-4ce6e1379d594ca39d30833816295b61 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-20T21:48:47Z |
| publishDate | 2021-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-4ce6e1379d594ca39d30833816295b612022-12-21T19:25:36ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-11-011210.3389/fpls.2021.773090773090Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication SignatureLian-Ying Shen0Hang Luo1Xiao-Ling Wang2Xue-Meng Wang3Xiao-Jing Qiu4Hui Liu5Shan-Shan Zhou6Kai-Hua Jia7Shuai Nie8Yu-Tao Bao9Ren-Gang Zhang10Quan-Zheng Yun11Ying-Hui Chai12Jin-Ying Lu13Yu Li14Shu-Wei Zhao15Jian-Feng Mao16Shan-Gang Jia17Yong-Min Mao18Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaResearch Center of Chinese Jujube, Hebei Agricultural University, Baoding, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaResearch Center of Chinese Jujube, Hebei Agricultural University, Baoding, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaBeijing Ori-Gene Science and Technology Co., Ltd., Beijing, ChinaBeijing Ori-Gene Science and Technology Co., Ltd., Beijing, ChinaBeijing Ori-Gene Science and Technology Co., Ltd., Beijing, ChinaShenzhou Space Biotechnology Group, China Academy of Space Technology (CAST), Beijing, ChinaInstitute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing, ChinaHebei Hemuliyuan Agricultural Science and Technology Co. Ltd., Baoding, ChinaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaResearch Center of Chinese Jujube, Hebei Agricultural University, Baoding, ChinaSour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.https://www.frontiersin.org/articles/10.3389/fpls.2021.773090/fullsour jujubegenome assemblystress responsefruitsselective sweep |
| spellingShingle | Lian-Ying Shen Hang Luo Xiao-Ling Wang Xue-Meng Wang Xiao-Jing Qiu Hui Liu Shan-Shan Zhou Kai-Hua Jia Shuai Nie Yu-Tao Bao Ren-Gang Zhang Quan-Zheng Yun Ying-Hui Chai Jin-Ying Lu Yu Li Shu-Wei Zhao Jian-Feng Mao Shan-Gang Jia Yong-Min Mao Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature Frontiers in Plant Science sour jujube genome assembly stress response fruits selective sweep |
| title | Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature |
| title_full | Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature |
| title_fullStr | Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature |
| title_full_unstemmed | Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature |
| title_short | Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature |
| title_sort | chromosome scale genome assembly for chinese sour jujube and insights into its genome evolution and domestication signature |
| topic | sour jujube genome assembly stress response fruits selective sweep |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.773090/full |
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