Figure 10

Representative comparisons of obtained cDNA, amphioxus genomic DNA, and gene models. The comparison of obtained cDNA with amphioxus genomic DNA scaffolds and gene models reveals problems with the gene models. In panels A, B, D, and E, the upper black band with coordinates represents part of the genomic scaffold. Red segmented boxes above the genomic scaffolds represent gene models. The lower black band represents cDNA. Exons are shown as cyan segmented boxes. Predicted exons not present in cDNA are labeled with ‘x’. Predicted exons with no evidence of existence are labeled with ‘?’. (A) The comparison of BfArnt cDNA, the corresponding genomic scaffold, and gene model 124387. This shows that, based on the model, the predicted structure of exon/intron is incorrect, and the model does not involve a putative translation stop. (B) The comparison of BfNpas1/3 cDNA, the corresponding genomic scaffold, and gene models. This shows that those models lack the correct translation start and that four separate models should be combined to represent a single gene. (C-E) The comparison of BfHifα cDNA and the two corresponding genomic regions shows the redundancy of models. In panel C, the upper schematic figure (not to scale) shows the positional relationships of two BfHifα models (red boxes) and their neighboring gene models (black boxes), and the X-Y plot shows the comparisons of two scaffold regions denoted by blue lines. Synteny of gene models on each scaffold region and sequence similarity show the redundancy of the gene models. Panels D and E show the comparison of BfHifα cDNA (long isoform), the genomic scaffolds, and gene models 208339 and 208408. In E, the black boxes on the genomic scaffold are ambiguous gap regions, which were not sequenced and were denoted as strings of ‘N’s in the genome browser. The cDNA region not aligned may be due to these regions.