Due to the large amount of ncRNA reads, another assembly was conducted using the Newbler program (Roche) which incorporated filtering for structural RNAs, low quality reads, and abbreviated reads. The BLAST cut-off e-value used in the filtering ncRNAs was set at e-50, resulting in 349,613 out of 1,406,316 reads in total to be removed prior to assembly. Again, assemblies were conducted for the 5 BBD-resistant libraries, the 5 BBD-susceptible libraries, and all 10 libraries combined.