中国农业大学韩振海研究组近日取得一项新成果。他们的研究显示，泛基因组分析揭示了苹果的进化和多样性。该项研究成果发表在2025年4月16日出版的《自然—遗传学》上。

该课题组人员测序并组装了30个高质量的苹果基因组，代表了20个二倍体和10个多倍体，跨越了主要的进化谱系和地理区域。系统基因组学分析揭示了古代基因的复制和转换，而六种新定义的基因组类型，包括多倍体物种共享的祖先类型，有助于检测广泛渗入的强信号。基于图谱的泛基因组捕获了共享的和物种特异性的结构变异，促进了苹果抗痂病分子标记的开发。他们对选择性扫描的分析发现，在驯化过程中，MdMYB5突变降低了抗寒性和抗病性。这项研究推进了苹果基因组学，揭示了遗传多样性和进化见解，同时加强了理想性状的育种。

据介绍，Malus Mill是一种具有重要农业和生态价值的温带多年生乔木属，通过杂交、多倍体和环境适应等途径实现了多样性。有限的基因组资源阻碍了对其进化历史和遗传多样性的认识。

附：英文原文

Title: Pan-genome analysis reveals the evolution and diversity of Malus

Author: Li, Wei, Chu, Chong, Zhang, Taikui, Sun, Haochen, Wang, Shiyao, Liu, Zeyuan, Wang, Zijun, Li, Hui, Li, Yuqi, Zhang, Xingtan, Geng, Zhiqiang, Wang, Youqing, Li, Yi, Zhang, Hengtao, Fan, Weishu, Wang, Yi, Xu, Xuefeng, Cheng, Lailiang, Zhang, Dehui, Xiong, Yao, Li, Huixia, Zhou, Bowen, Guan, Qingmei, Deng, Cecilia H., Han, Yongming, Ma, Hong, Han, Zhenhai

Issue&Volume: 2025-04-16

Abstract: Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.

DOI: 10.1038/s41588-025-02166-6

Source: https://www.nature.com/articles/s41588-025-02166-6