Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii

Junhui Yuan (), Sanjie Jiang, Jianbo Jian, Mingyu Liu, Zhen Yue, Jiabao Xu, Juan Li, Chunyan Xu, Lihong Lin, Yi Jing, Xiaoxiao Zhang, Haixin Chen, Linjuan Zhang, Tao Fu, Shuiyan Yu, Zhangyan Wu, Ying Zhang, Chongzhi Wang, Xiao Zhang, Liangbo Huang, Hongqi Wang, Deyuan Hong (), Xiao-Ya Chen () and Yonghong Hu ()
Additional contact information
Junhui Yuan: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Sanjie Jiang: BGI Genomics, BGI-Shenzhen
Jianbo Jian: BGI Genomics, BGI-Shenzhen
Mingyu Liu: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Zhen Yue: BGI Genomics, BGI-Shenzhen
Jiabao Xu: BGI Genomics, BGI-Shenzhen
Juan Li: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Chunyan Xu: BGI Genomics, BGI-Shenzhen
Lihong Lin: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Yi Jing: BGI Genomics, BGI-Shenzhen
Xiaoxiao Zhang: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Haixin Chen: BGI Genomics, BGI-Shenzhen
Linjuan Zhang: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Tao Fu: BGI Genomics, BGI-Shenzhen
Shuiyan Yu: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Zhangyan Wu: BGI Genomics, BGI-Shenzhen
Ying Zhang: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Chongzhi Wang: BGI Genomics, BGI-Shenzhen
Xiao Zhang: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden
Liangbo Huang: BGI Genomics, BGI-Shenzhen
Hongqi Wang: BGI Genomics, BGI-Shenzhen
Deyuan Hong: Institute of Botany, Chinese Academy of Sciences
Xiao-Ya Chen: Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences
Yonghong Hu: the Chinese Academy of Science, Shanghai Chenshan Botanical Garden

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract Tree peony (Paeonia ostii) is an economically important ornamental plant native to China. It is also notable for its seed oil, which is abundant in unsaturated fatty acids such as α-linolenic acid (ALA). Here, we report chromosome-level genome assembly (12.28 Gb) of P. ostii. In contrast to monocots with giant genomes, tree peony does not appear to have undergone lineage-specific whole-genome duplication. Instead, explosive LTR expansion in the intergenic regions within a short period (~ two million years) may have contributed to the formation of its giga-genome. In addition, expansion of five types of histone encoding genes may have helped maintain the giga-chromosomes. Further, we conduct genome-wide association studies (GWAS) on 448 accessions and show expansion and high expression of several genes in the key nodes of fatty acid biosynthetic pathway, including SAD, FAD2 and FAD3, may function in high level of ALAs synthesis in tree peony seeds. Moreover, by comparing with cultivated tree peony (P. suffruticosa), we show that ectopic expression of class A gene AP1 and reduced expression of class C gene AG may contribute to the formation of petaloid stamens. Genomic resources reported in this study will be valuable for studying chromosome/genome evolution and tree peony breeding.

Date: 2022
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DOI: 10.1038/s41467-022-35063-1

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