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“Breeding on mountains, cultivation in dam areas” is a unique propagation method for the vegetatively propagated plant  Ligusticum chuanxiong , including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on  L. chuanxiong  and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in  L. chuanxiong  increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of  L. chuanxiong , while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant  Gibberella ,  Phoma ,  Pericona ,  Paraphoma , and  Neocosmospora . The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.

“Breeding on Mountains” Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants (Ligusticum chuanxiong Hort.)