Genome Concatenation Enables Accurate Dual RNA-seq mapping for lignocellulolytic fungi in coculture
Sample preparation and collectionMycelia from cocultures were harvested via filtration after the 6-day growth period and flash frozen in liquid nitrogen. Total RNA isolation from the two organisms was isolated with PureLinkPlant RNA Reagent (Invitrogen  ThermoFisher Scientific, Waltham, MA, USA), followed by purification using the Direct-zol RNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA) following the manufacturers instructions. RNA integrity was verified by agarose gel electrophoresis and quantification via NanoDrop One Microvolume spectrophotometry (ThermoFisher Technologies, Waltham, MA, USA), employing a quality cut-off value of 1.8 for A260:280 ratios. RNA integrity was also measured on an Agilent 2100 Bioanalyzer system (Agilent Technologies, Palo Alto, CA, USA).RNA sequencingRNA samples from the coculture replicates were sequenced as paired-end reads (2 x 150 bp) using NovaSeq 6000 sequencing technology.