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Genomes of autotetraploid wild and cultivated Ziziphus mauritiana reveal polyploid evolution and crop domestication

文献类型： 外文期刊

作者： Guo, Mingxin 1 ; Bi, Guiqi 2 ; Wang, Huan 2 ; Ren, Hui 5 ; Chen, Jiaying 6 ; Lian, Qun 2 ; Wang, Xiaomei 5 ; Fang, Weikuan 5 ; Zhang, Jiangjiang 2 ; Dong, Zhaonian 2 ; Pang, Yi 1 ; Zhang, Quanling 2 ; Huang, Sanwen 2 ; Yan, Jianbin 2 ; Zhao, Xusheng 1 ;

作者机构： 1.Luoyang Normal Univ, Coll Life Sci, Luoyang 471934, Peoples R China

2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr & Rural Affairs, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr,K, Shenzhen 518124, Peoples R China

3.South China Agr Univ, Integrat Microbiol Res Ctr, Guangdong Prov Key Lab Microbial Signals & Dis Con, Guangzhou 510642, Peoples R China

4.South China Agr Univ, Coll Plant Protect, Guangzhou 510642, Peoples R China

5.Guangxi Acad Agr Sci, Hort Res Inst, Nanning 530007, Peoples R China

6.Chinese Acad Trop Agr Sci, South Subtrop Crops Res Inst, Zhanjiang 524000, Peoples R China

期刊名称：PLANT PHYSIOLOGY （ 影响因子：6.9； 五年影响因子：7.7 ）

ISSN： 0032-0889

年卷期： 2024 年 196 卷 4 期

页码：

收录情况： SCI

摘要： Indian jujube (Ziziphus mauritiana) holds a prominent position in the global fruit and pharmaceutical markets. Here, we report the assemblies of haplotype-resolved, telomere-to-telomere genomes of autotetraploid wild and cultivated Indian jujube plants using a 2-stage assembly strategy. The generation of these genomes permitted in-depth investigations into the divergence and evolutionary history of this important fruit crop. Using a graph-based pan-genome constructed from 8 monoploid genomes, we identified structural variation (SV)-FST hotspots and SV hotspots. Gap-free genomes provide a means to obtain a global view of centromere structures. We identified presence-absence variation-related genes in 4 monoploid genomes (cI, cIII, wI, and wIII) and resequencing populations. We also present the population structure and domestication trajectory of the Indian jujube based on the resequencing of 73 wild and cultivated accessions. Metabolomic and transcriptomic analyses of mature fruits of wild and cultivated accessions unveiled the genetic basis underlying loss of fruit astringency during domestication of Indian jujube. This study reveals mechanisms underlying the divergence, evolution, and domestication of the autotetraploid Indian jujube and provides rich and reliable genetic resources for future research. A 2-stage assembly strategy reveals the assemblies of haplotype-resolved, telomere-to-telomere genomes of autotetraploid wild and cultivated Indian jujube plants.

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