Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

作者：Mingjin Huang, Shanshan Luo, Linshuang Tang, Hao Yin, Daliang Liu, Zhipeng Li, Qiyu Chen, Yinjie Jiao, Mengge Li, Yanlin Hao, Tao Li, Dachang Wang, Hongchang Liu, Dandan Li, Jin He, Lin Cheng, Cheng Li, Hualei Wang, Guojin Zhang, W Wang, Ruimin Wang, Xinhao Sun, Yiyong Zhao · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2026 · DOI：10.64898/2026.01.26.701689 · 研究领域：Biological and pharmacological studies of plants、Plant Molecular Biology Research、Plant biochemistry and biosynthesis

Abstract Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata , a medicinal orchid forming long-term symbioses with Armillaria and Mycena , provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata -fungus mutualism is sustained through metaboli...