Genome Concatenation Enables Accurate Dual RNA-seq mapping for lignocellulolytic fungi in coculture

Dual RNA-seq enables simultaneous transcriptome profiling of interacting organisms,yet accurate read assignment remains challenging, particularly in fungal cocultureswhere phylogenetic proximity and high percentages of homologous sequences can beshared. Here, we evaluate two mapping strategies for dual RNA-seq analysis ofTrichoderma reesei RUT-C30 and Pleurotus citrinopileatus cocultivated on sugarcanebagasse, based on a sequential alignment against individual genomes and aconcatenated reference genome approach.