Jiang Nan, Li Zhenhao, Dai Yueting, Liu Zhenhua, Han Xuerong, Li Yu, Li Yong, Xiong Hui, Xu Jing, Zhang Guoliang, Xiao Shijun, Yuan Xiaohui, Fu Yongping
International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China.
College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China.
Mol Ecol Resour. 2022 Oct 10. doi: 10.1111/1755-0998.13718.
Genome introgression is one of the driving forces that can increase species and genetic diversity and facilitate the adaptive evolution of organisms and biodiversity conservation. However, the genomic introgression and its contribution to biodiversity of macrofungi are still unclear. The genus Ganoderma is a typical macrofungal group that plays crucial roles in forest ecosystem as saprophytic organisms and plant pathogens, and is also involved in human health as medicinal mushrooms. Most public Ganoderma genomes are fragmented, and reference genomes and whole-genome information of diverse germplasm resources for many Ganoderma species are lacking, thus hindering functional and evolutionary genomic investigations among Ganoderma species. In this study, we provide high-quality genomes of 10 Ganoderma species and whole-genome variants data of 224 individuals from various ecoregions, enabling us to infer the phylogeny of Ganoderma species and their historical population dynamics. Based on whole-genome variants, widespread and genome-wide introgression among Ganoderma species is revealed. Genes with significant introgression signals were related to stress response, digestive absorption, and secondary metabolite synthesis, factors that may contribute to environmental adaptation and important biocomponent metabolism. CYP512U6, an essential functional gene in the CYP450 family related to Ganoderma triterpene synthesis, was detected with significant introgression and selection signals combined with Ganoderma metabolomic analysis, indicating that both ancient gene exchange and recent domestication have contributed to the categories and content of secondary metabolites of Ganoderma. The reference genomes, whole-genome variants, and metabolite profiles could serve as abundant and valuable genetic resources for evolution, ecology, and conservation investigations of Ganoderma species and other macrofungi.
基因组渐渗是增加物种和遗传多样性、促进生物适应性进化及生物多样性保护的驱动力之一。然而，大型真菌的基因组渐渗及其对生物多样性的贡献仍不清楚。灵芝属是典型的大型真菌类群，作为腐生生物和植物病原体在森林生态系统中发挥着关键作用，同时作为药用真菌也与人类健康相关。大多数公开的灵芝基因组是碎片化的，许多灵芝物种缺乏参考基因组和多样种质资源的全基因组信息，这阻碍了灵芝物种间的功能和进化基因组学研究。在本研究中，我们提供了10个灵芝物种的高质量基因组以及来自不同生态区域的224个个体的全基因组变异数据，使我们能够推断灵芝物种的系统发育及其历史种群动态。基于全基因组变异，揭示了灵芝物种间广泛的全基因组渐渗现象。具有显著渐渗信号的基因与应激反应、消化吸收和次生代谢物合成有关，这些因素可能有助于环境适应和重要生物成分的代谢。结合灵芝代谢组学分析，检测到参与灵芝三萜合成的CYP450家族中的一个关键功能基因CYP512U6具有显著的渐渗和选择信号，表明古老的基因交换和近期的驯化都对灵芝次生代谢物的种类和含量产生了影响。这些参考基因组、全基因组变异和代谢物谱可为灵芝物种及其他大型真菌的进化、生态和保护研究提供丰富且有价值的遗传资源。
