J Integr Plant Biol. ›› 2022, Vol. 64 ›› Issue (8): 1487-1501.DOI: 10.1111/jipb.13318

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Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

Ticao Zhang1†*, Qin Qiao2†*, Xiao Du3,4, Xiao Zhang3, Yali Hou3, Xin Wei3, Chao Sun3, Rengang Zhang5, Quanzheng Yun5, M. James C. Crabbe6,7,8, Yves Van de Peer9,10,11 and Wenxuan Dong3*   

  1. 1 College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
    2 School of Agriculture, Yunnan University, Kunming 650091, China
    3 College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
    4 Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Guangxi, Nanning 530001, China
    5 Beijing Ori‐Gene Science and Technology Co. Ltd, Beijing 102206, China
    6 Wolfson College, Oxford University, Oxford, UK
    7 Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Park Square, Luton, UK
    8 School of Life Sciences, Shanxi University, Taiyuan 030006, China
    9 Department of Plant Biotechnology and Bioinformatics, Center for Plant Systems Biology, Ghent University, VIB, 9052, Ghent, Belgium
    10 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
    11 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China

    These authors contributed equally to this work.
    *Correspondences: Ticao Zhang (ticaozhang@126.com, Dr. Zhang is fully responsible for the distribution of the materials associated with this article), Qin Qiao (qiaoqin@ynu.edu.cn) and Wenxuan Dong (wxdong63@126.com)
  • Received:2022-04-18 Accepted:2022-06-13 Online:2022-06-24 Published:2022-08-01


Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar “Qiu Jinxing.” We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.

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