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Phylogenomics from 481 nuclear genes and plastomes refines infrageneric classification and species delimitation in Chinese hawthorns (Crataegus, Rosaceae)

Jia-Xin Huang1,2,3†, Si-Yu Xie2,3,4†, Ya-Wen Zheng2,3,5†, Dai-Kun Ma2,3,6, Xiao-Ya Li2,3,6, Shuai Liao7, Liang Zhao4, Chao Xu2,3, Jing-Hong Wang5, Jin Cheng1*, Bin-Jie Ge8*, James B. Phipps9*, and Bin-Bin Liu2,3*   

  1. 1National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
    2Key Laboratory of Systematic and Evolutionary Botany/State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
    3China National Botanical Garden, Beijing 100093, China
    4College of Life Sciences & Herbarium of Northwest A&F University, Northwest A&F University, Yangling 727100, China
    5College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China
    6University of Chinese Academy of Sciences, Beijing 100049, China
    7Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
    8Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
    9Department of Biology, The University of Western Ontario, London, Ontario, Canada
    †These authors contributed equally to this work.
    *Authors for correspondence. Bin-Bin Liu. E-mail: liubinbin@ibcas.ac.cn; James B. Phipps. E-mail: jphipps@uwo.ca; Bin-Jie Ge. E-mail: gebinjie123@163.com; Jin Cheng. E-mail: chengjin@bjfu.edu.cn
  • Received:2025-10-21 Accepted:2026-01-13
  • Supported by:
    Financial support for this work was provided by the National Natural Science Foundation of China (grant number 32270216 to BBL and 32000163 to BBL), the Youth Innovation Promotion Association, Chinese Academy of Sciences (2023086 to BBL), and the Biological Resources Programme, Chinese Academy of Sciences (CAS-TAX-24-013 to BBL).

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Abstract: Crataegus L. (hawthorns) is a taxonomically challenging genus within the Rosaceae family, exhibiting extensive morphological variation, frequent hybridization, and polyploidy. In China, about 18 species are currently recognized, but their subgeneric classification and species boundaries remain unresolved. To clarify these relationships, we analyzed 481 nuclear genes, 73 plastid coding sequences, and a comprehensive plastome dataset for 17 Chinese Crataegus species. Phylogenomic analyses of both nuclear and plastid data yielded well-supported trees that refine the taxonomy and elucidate evolutionary relationships within the genus. All Chinese species are resolved within two subgenera, C. subg. Crataegus and C. subg. Sanguineae, although most currently recognized species are not monophyletic, reflecting complex reticulate evolution involving hybridization and polyploidy. Integrating phylogenomic, morphological, and cytological evidence, we provide an updated taxonomic synopsis of Chinese Crataegus, describe one new species, propose five new combinations, and designate 31 lectotypes. This study establishes a robust framework for future systematic, conservation, and horticultural research on this ecologically and economically important lineage.

Key words: Chinese hawthorns, Crataegus, morphology, phylogenomics, taxonomy

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