Fig. 3

Repetitive sequences in the Sp185/333 gene clusters are assembled correctly by PacBio but not by Illumina. Five BAC insert assemblies are compared to self by pairwise alignments and illustrated as dot plots. Lines and dots that are displaced from the central diagonal are repetitive sequences that include Sp185/333 gene sequences (regions with displaced diagonals are indicated with boxes) and STRs (dots). a The Sp185/333 gene clusters assembled from Illumina reads for BAC assemblies corresponding to Clusters 1, 2 and 3 have Sp185/333 genes that are fragmented and shorter than expected (the displaced diagonals are composed of short lines or dots) based on gene size predictions (not shown) and according to previous reports [20, 21]. b The Sp185/333 gene clusters assembled from PacBio reads for BACs compared to self. The PacBio assemblies show intact and longer displaced diagonals representing genes of expected length. The orientations of the genes are indicated by the displaced diagonals are either parallel (same orientation) or perpendicular (opposite orientation) to the central diagonal