Total RNA was isolated from Stage 3–6 FBs. Double-stranded cDNA was synthesized and amplified using the SMART PCR cDNA Synthesis Kit (Ozyme, Saint-Quentin-en-Yvelines, France), according to the manufacturer’s instructions, and used for hybridizations to NimbleGen oligoarrays2. Single dye labeling of samples, hybridization procedures, and data acquisition were performed at the NimbleGen facilities (NimbleGen Systems, Reykjavik, Iceland) following their standard protocol. The T. melanosporum custom-exon expression array (GPL8982) manufactured by Roche NimbleGen Systems (Madison, WI, USA) contained five independent, non-identical, 60-merprobes per gene model coding sequence. Included in the oligoarray were 7496 annotated protein-coding gene models, 5736 TE sequences, 3913 random 60-mer control probes, and labeling controls. For 1876 gene models, technical duplicates were included in the array.