Mapping of the reads from each library onto the assembled transcriptomes revealed a high level of several sequences of ribosomal origins. These transcripts accounted for 34% (180,292 out of 533,261), 27% (139,718 out of 521,505) and 18% (186,745 out of 1,026,995) of the resistant, susceptible and combined assemblies, respectively. To determine the amount of structural non-coding RNA (ncRNA) sequences present in the libraries, the RFAM structural RNA database  was downloaded to serve as a local BLAST database. All of the sequence reads and contig sequences in the three assembled transcriptomes were aligned to the RFAM database, using a conservative BLAST e-value threshold of e-70, the ribosomal content was about 30% of the sequenced reads. ncRNAs accounted for 729, 1506 and 2110 contigs for the resistant, susceptible and combined assemblies, respectively. These contigs were removed from the assemblies, prior to SNP discovery.