Genomes of autotetraploid wild and cultivated <i>Ziziphus mauritiana</i> reveal polyploid evolution and crop domestication
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.
Authors
- Xusheng Zhao (ORCID: https://orcid.org/0000-0002-2011-6217)
- Jianbin Yan (ORCID: https://orcid.org/0000-0001-7934-8808)
- Ren Hui (ORCID: https://orcid.org/0009-0003-7415-1194)
- Mingxin Guo (ORCID: https://orcid.org/0000-0002-7764-1194)
- Sanwen Huang (ORCID: https://orcid.org/0000-0002-8547-5309)
- Zhaonian Dong
- Jiangjiang Zhang (ORCID: https://orcid.org/0000-0002-9647-5101)
- Quanling Zhang (ORCID: https://orcid.org/0009-0003-2177-1824)
- Xiaomei Wang (ORCID: https://orcid.org/0000-0003-0855-7498)
- Jiaying Chen (ORCID: https://orcid.org/0000-0002-5340-9999)
- Huan Wang (ORCID: https://orcid.org/0009-0002-5692-0474)
- Qun Lian (ORCID: https://orcid.org/0000-0001-8734-8357)
- Weikuan Fang (ORCID: https://orcid.org/0009-0008-6682-2732)
- Guiqi Bi (ORCID: https://orcid.org/0000-0003-3067-5765)
- Yi Pang
Institutions
- South China Agricultural University (CN)
- Chinese Academy of Tropical Agricultural Sciences (CN)
- Agricultural Genomics Institute at Shenzhen (CN)
- Horticultural Research Institute (US)
- Luoyang Normal University (CN)
- Guangxi Academy of Agricultural Science (CN)
- South Subtropical Crops Research Institute (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Ministry of Agriculture and Rural Affairs (CN)
Publication Details
- Journal
- PLANT PHYSIOLOGY
- Published
- 2024-09-26
- DOI
- https://doi.org/10.1093/plphys/kiae512
- Citations
- 8
- Primary Topic
- Ziziphus Jujuba Studies and Applications
- Type
- article
- Field-Weighted Citation Impact
- 2.79
Funders
- National Natural Science Foundation of China
- Chinese Academy of Agricultural Sciences
- Luoyang Normal University
- National Key Research and Development Program of China