The sequencing of 10 cDNA libraries yielded 1,406,316 reads covering 508,764,432 bases. The libraries from BBD-resistant trees yielded between 87,964 and 210,340 reads, while 70,218 to 205,945 reads were obtained for libraries from BBD-susceptible trees (Table 1). While the quality and quantity of the sequence data was acceptable (Table 1; Additional file 2), the mRNA poly-A selection step left a large proportion of structural non-coding RNAs in the samples, including ribosomal RNA. Moreover, up to a third of the transcriptome sequence reads were mapped to ncRNAs. Subsequently, the quality of the mRNA preparations was re-assessed with an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies), revealing remnant rRNA peaks (Additional file 3). Because the ncRNA contamination was detected after the first transcript assemblies were conducted, a second assembly with additional filtering was conducted (see below).Table 1Result metrics for the sequencing of 10 beech cDNA librariesLibrary Name (based on tree number)Number of readsAverage read lengthTotal basesBBD-Resistant trees Beech_1228R210,34037578,912,594 Beech_2692R131,30635446,467,779 Beech_1504R123,19437045,498,709 Beech_1208R87,96435831,467,605 Beech_2276R147,78137455,192,118Resistant tree Sub-Totals700,585366.2257,538,805BBD-Susceptible trees Beech_1973S205,94535873,702,265 Beech_DN00726S159,66034955,759,976 Beech_3128S130,91735946,933,567 Beech_2143S138,99135749,586,742 Beech_Holden70,21836025,243,077Susceptible tree Sub-Totals705,731356.6251,225,627Totals for all libraries1,406,316361508,764,432