TABLE 3.

Selected examples of plant gene alteration in the presence of endophytic fungi (EFs) and their resulted beneficial expression.

Host Plant	Endophytic fungal community	Gene ontology (up regulation/down regulation)	Phenotypic expression/gene function	References
Taxus (young/old plantlets)	Paraconiothyrium SSM001	Up regulation of TS, DXR, HMGR genes (related to taxol synthesis)	Increase the concentration of host plant taxol	Soliman et al., 2013
Soybean plant (Glycine max)	P. indica	61 genes are up- regulation and 238 genes are down-regulated	Enhancing the iron transport, lignin biosynthesis, hormone signaling, nutrient acquisition, biosynthesis of phenylpropanoids, flavonols, siderophores, and flavonoids (61 genes) 238 genes involved in encoding the heat shock protein, and several other abiotic stress related defense responses	Bajaj et al., 2018
Rhodiola crenulata	Trimmatostroma sp. ZPRs-R11	Up regulatory genes are TYDC, MAOA, C4H, TAT, PAL, PCD	Induced the accumulation of tyrosol and salidroside	Cui et al., 2017
Lolium perenne (perennial ryegrass)	N. lolii	Up regulation of MRP/PDR like ABC and GST transporter systems related genes and downregulation of carbohydrate metabolism and photosynthesis related genes	Activates the cellular transport, transporter system, protein synthesis.	Khan et al., 2010
Hordeum vulgare L. (barley)	P. indica	PR-5 gene	Induced tolerance in salt stress and the systemic disease resistance via elevating the conc. of antioxidant metabolites (ascorbate-glutathione pathway).	Waller et al., 2005