Comparative transcriptomics (RNA-Seq) of Trifolium pratense roots infected with the fungal pathogens Fusarium oxysporum or Phoma medicaginis

Fungal infection broadly activated both core metabolic processes and specialized metabolic pathways, including transcripts encoding phenylpropanoid and (iso)flavonoid biosynthetic enzymes. Among 33 predicted isoflavonoid-pathway genes, many were differentially expressed in at least one fungal treatment, with the late steps of pterocarpan biosynthesis particularly induced by P. medicaginis.

These comparative transcriptomes provide insight into the activation and regulation of biotic stress responses as well as the engagement of legume-specific isoflavonoid biosynthesis, a pathway closely linked to antimicrobial defense.