Figure 5

Multiple amplification products from Euglena genomic PCR reveal U3 snoRNA-U5 snRNA gene linkages that cluster into related families and sub-families. (A) PCR amplification of total Euglena DNA with primers designed to the 5'-regions of the convergently oriented U3 snoRNA and U5 snRNA genes (oEg U3-F1 and oEg U5-F1; see Additional file 2) yields multiple amplification products ranging in size from ~425 to ~550 bp. (B) Alignment of PCR products demonstrates high sequence conservation of the U3 snoRNA and U5 snRNA genes, both within a linkage family and between linkage families. Numbers at the ends of the alignments indicate the percent sequence identity (% ID) among family members within the IGS, excluding the U3 and U5 coding sequences and putative transcription termination signals. Family members that are identical within the IGS may nevertheless display nucleotide heterogeneities within the flanking U3 or U5 genes. The alignment begins at nt 10 of the U3 snoRNA gene, owing to the location of the PCR primer.