Comparison of the protein domain architecture of zebrafish WGD-duplicates and those of their single mouse ortholog. (A) A total of 493 zebrafish gene pairs could be annotated with protein domain information when searched against the Pfam-A database of known protein domain motifs, with the majority of gene pairs (422) encoding the same types and number of domains. (B) The 71 zebrafish gene pairs that differed in domain architecture were compared to their single mouse ortholog to infer whether duplicate gene copies had lost or gained a domain compared with the ancestral locus. In seven comparisons where duplicate zebrafish genes differed in the types of domains encoded, we found evidence for the missing domains at the genomic sequence level, even if the transcripts or proteins encoding these domains have not yet been observed. These are indicated by gray boxes in the diagram. For seven other gene pairs, there were no orthologs in mouse.
