Total Transcriptome Expression
Prior to assembly, FASTQ files generated by Illumina sequencing were processed to remove any adapter or low quality sequences (we trimmed reads with a quality score of less than 28 from the end of each read, and removed entirely both read mate-pairs for which this procedure resulted in a sequence less than 60 nucleotides from either of the read mate-pairs).  The FastQC package was used to verify the quality of the resulting trimmed and filtered reads.