Study of bacterial-fungal host co-infection
The reads were aligned to each reference genome (M. restricta reference; GCF_003290485.1_ASM329048v1) using HISAT2 (version 2.1.0) alignment software (Langmead et al., 2009). Raw read counts were generated using StringTie (version 2.1.3b) for each annotated gene. Differentially expressed gene (DEG) analysis was performed using EdgeR for comparative combinations (axenic- and co-treatment samples).