Gene expression changes in three Pisolithus microcarpus monokaryon strains and one dikaryon strain during colonisation of Poplar roots compared to free-living mycelium.
Illumina  technology was used to generate mRNA profiles of three Pisolithus microcarpus monokaryon (M057, M091, and M120) and one dikaryon (D002) strains. Total RNAs was extracted from ectomycorrhizal (ECM) tissues and free-living mycelium (FLM) using a CTAB and lithium chloride (LiCl)-based method.TruSeq mRNA Stranded libraries were constructed and 2 x 125 bp sequenced using Illumina HiSeq 2500 at the Genotoul sequencing facilities (Toulouse, France).Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the P. microcarpus 441 v. 2 primary scaffolds reference transcripts available at the JGI database  (https://mycocosm.jgi.doe.gov) using CLC Genomics Workbench 21.0.3. Overall design: mRNA profiles of of three Pisolithus microcarpus monokaryon (M057, M091, and M120) and one dikaryon (D002) strains were generated by Illumina HiSeq 2500 (2x125bp). Three biological replicates were sequenced.