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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Autores principales: 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
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Publicado: Frontiers Media S.A. 2021
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Acceso en línea:https://doaj.org/article/4ce6e1379d594ca39d30833816295b61
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spelling 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)
institution DOAJ
collection DOAJ
language EN
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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