Expression levels of black widow reference genes. Total sense (turquoise) and antisense (salmon) transcript abundance for genes with an observed tag more abundant in major ampullate (MA) glands than cephalothoraxes (FDR ≤ 0.05). Transcript abundance is the sum of the average log counts per million (cpm) of all tags that matched to that gene between two MA libraries. Reference genes are ranked according to decreasing total abundance. Rank abundance according to just the 3′-most tag (rank 3′) is almost identical (see also Additional file 1: Figure S6c). Genes that were not significantly different according to the 3′-most tag are marked with an asterisk (*). Descriptor is the top BLASTX hit to NCBI non-redundant (nr) protein database. Bolded genes have a signal peptide predicted by SignalP using D-value cut off = “sensitive”. aOnly BLASTX hits are hypothetical proteins in L. hesperus. bContig5 and Lnc168 are nearly identical for the first 178 bases. Tags are located downstream in regions that do not align between the two sequences. cContig31 and HQ005922 align with 42% identity over 43 amino acids. dHQ006066 and HQ006098 align with 47% identity over 54 amino acids. eAligns to hypothetical proteins from multiple species using BLASTX. fThese four sequences align with ~73-95% pairwise identity over the entire amino acid sequence (81-93 amino acids). Contig43, Contig30 and HQ006054 share a tag. Contig43 and HQ006044 share an additional tag. HQ006044 has a predicted tag in the same location as the other three, but it is not observed.