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...
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Frontiers Media S.A.
2021
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oai:doaj.org-article:4ce6e1379d594ca39d30833816295b612021-11-30T19:08:20ZChromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature1664-462X10.3389/fpls.2021.773090https://doaj.org/article/4ce6e1379d594ca39d30833816295b612021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.773090/fullhttps://doaj.org/toc/1664-462XSour 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.Lian-Ying ShenHang LuoXiao-Ling WangXue-Meng WangXiao-Jing QiuHui LiuShan-Shan ZhouKai-Hua JiaShuai NieYu-Tao BaoRen-Gang ZhangQuan-Zheng YunYing-Hui ChaiJin-Ying LuYu LiShu-Wei ZhaoJian-Feng MaoShan-Gang JiaYong-Min MaoFrontiers Media S.A.articlesour jujubegenome assemblystress responsefruitsselective sweepPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021) |
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| topic |
sour jujube genome assembly stress response fruits selective sweep Plant culture SB1-1110 |
| spellingShingle |
sour jujube genome assembly stress response fruits selective sweep Plant culture SB1-1110 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 |
| 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. |
| format |
article |
| 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 |
| title |
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_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_sort |
chromosome-scale genome assembly for chinese sour jujube and insights into its genome evolution and domestication signature |
| publisher |
Frontiers Media S.A. |
| publishDate |
2021 |
| url |
https://doaj.org/article/4ce6e1379d594ca39d30833816295b61 |
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