RNA-Seq of Fungi on Nutrient Media

Conidia from strains grown two weeks on ½ strength corn meal agar and 1 × 10⁶ spores were inoculated into 100 mL of both Czapek-Dox broth and SM producing media [79 (link)]. Two replicate flasks were grown for each strain. Tissue for RNA extraction was harvested at 7 days and RNA was extracted using TRIzol (Invitrogen) according to the manufactures protocol. RNA libraries were prepared using the TruSeq RNA kit and sequenced as a depth of 12 multiplexed samples per lane on the Illumina Hi-Seq 2500 PE with 100 bp reads. RNA-Seq reads were first trimmed to 75 bp to remove poor quality reads at the beginning (15 bp) and end (10 bp) of the reads and reads with an average quality score of < 20 were removed. Transcripts were assembled using Trinity [80 (link)] and input into MAKER.