Abstract
BACKGROUND: Gastrodia elata Bl., commonly known as Tianma, is a perennial non-photosynthetic plant of the Orchidaceae family. Its growth and development rely on the symbiosis with at least two specific fungi. However, during artificial cultivation, it is prone to pathogen infection, which limits its industrial development. Currently, there is a lack of systematic research on the genomic composition, evolutionary characteristics, and regulatory mechanisms of the disease-resistant genes in Tianma. METHOD: The study focused on the genome of G. elata with a dark red phenotype. Pathogen recognition genes (PRGs) were systematically identified by integrating plant resistance gene databases, sequence homology searches, and domain verification. Phylogenetic relationships, chromosomal distribution, gene structure, conserved motifs, and repetitive events were analyzed. Additionally, the evolutionary conservation was evaluated through inter-species synteny analysis. Furthermore, cis-acting elements (CAEs) within the 2,000 bp promoter region were predicted, and expression patterns at different developmental stages and in different genotypes were analyzed based on transcriptomic data. RESULT: A total of 67 PRGs in G. elata (GePRGs) were identified, belonging to multiple gene families and exhibiting significant structural and evolutionary diversity. Tandem and fragment repeats both contributed to the expansion of this gene family, with six tandem repeat events detected. A total of 54 GePRGs showed significant syntenic relationships with homologous genes in other plants. The promoter region was found to contain 101 CAEs, which were enriched in MYB binding sites, dehydration-responsive elements, and low-temperature-responsive elements, suggesting their potential involvement in abiotic stress and pathogen defense responses. Expression analysis revealed that GeLRR-RLK12, GeLec-RLK15, and GeLRR-RLK28 were highly expressed during early developmental stages, while GeLRR-RLK24, GeLec-RLK2, GeLec-RLK3, and GeLec-RLK8 were continuously upregulated throughout development. The G. elata with light green stem (GELG) exhibited the highest overall expression levels of GePRGs, with GeLRR-RLK17, GeLRR-RLK36, GeLYK1, and GeLec-RLK13 showing particularly prominent expression. CONCLUSION: This study systematically analyzed the characteristics, evolutionary relationships, and expression patterns of GePRGs, which provide valuable genetic resources for disease-resistant breeding and the selection of superior germplasm in G. elata. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08343-x.