Validation of assemblies by Southern "dot" blot analysis. a) The top-most cartoon depicts overlapping BAC clones (light blue) which are predicted to span a chromosome (assembled from multiple scaffolds, dark blue). Genes (orange) are selected such that they link proposed contiguous scaffolds. These overlapping pairs of probes create a stair-stepping effect on the Southern blot if the hybridization results are as predicted (bottom), indicating that the linkage of the scaffolds, and thus the chromosome, is correct. b) TcChr20 was chosen for Southern blot validation. Overlapping BAC clones (grey) are selected such that they span most of the chromosome. Gene probes are shown in orange (ids shown are truncated forms of the "Tc" gene ids, i.e. 506581.10 denotes Tc00.1047053506851.10). While there are 11 previously published scaffolds linked on this chromosome, the red stars indicate a region containing many trans- sialidase genes whose repetitive nature must have hindered the joining of the 4 scaffolds that terminate in this region (2 large "P" scaffolds and 2 "S" scaffolds). c) For each BAC clone, both of the gene probes positively hybridize as predicted, creating the stair-step effect that confirms the linkage of the genes on the chromosome. BAC clones are labeled with their assigned ids from the CHORI library.