Transcriptomics analysis for elucidating the mechanism underlying the enhancement of Arabidopsis Thaliana growth by the endophytic fungus Clonostachys rosea

Endophytic fungi are nonpathogenic fungi that live symbiotically in the interior of healthy plant tissues and form mutualistic associations with their hosts. These fungi are critically involved in promoting plant development, strengthening plant uptake of nutrients, and improving plant resistance to biotic and abiotic stress conditions. Endophytic fungi improve plant growth by synthesizing phytohormones (e.g., auxins and gibberellins), solubilizing phosphorus, and enabling nitrogen fixation, thereby enhancing nutrient availability and root development. Previously, we isolated an endophytic fungal strain named AE16 from Actinidia eriantha Benth., a traditional Chinese medicinal plant; this strain was found to substantially stimulate Arabidopsis thaliana growth. Here, to investigate the underlying molecular mechanisms, we conducted transcriptome sequencing analysis and used bioinformatics tools to determine the transcriptome profiles of AE16-inoculated A. thaliana root tissues. We obtained 683 genes with differential expressions, including 391 and 292 upregulated and downregulated genes, respectively. We screened and validated 25 selected genes with a role in plant growth promotion (3 photosynthesis-related genes, 14 starch- and glucose metabolism-related genes, 6 plant hormone synthesis-related genes, and 2 cell transport-related genes). These genes, along with the ERF family of transcription factors, might have a crucial role in promoting A. thaliana growth. The strain AE16 was identified as Clonostachys rosea according to its morphological characteristics and ITS sequencing results. These results further clarify the mechanisms of the mutualistic association between A. thaliana and C. rosea and provide theoretical support to obtain sustained agricultural yield of other plants.