Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Figure 4
Distinct Dog Genes from Ensembl that Have Been Mispredicted as a Single Merged Chimera
(A) Ten predicted transcripts for a single Ensembl dog gene (ENSCAFG00000017952) on CFA 6. PhyOP orthology predictions suggest that only transcripts 1–4 highlighted in red are correct, and that these represent four distinct nonoverlapping dog in-paralogues (shaded in grey). Resolution of the transcript phylogeny strongly indicates that this one predicted gene is instead a composite of four true paralogous genes (in red; ENSCAFT00000028541, ENSCAFT00000028547, ENSCAFT00000028555, and ENSCAFT00000028561) and one pseudogene. At least five of the transcripts are chimeric constructs of exons from separate genes. In each and every case we examined, putative merged genes were the result of chimeric predicted transcripts sampling different combinations of exons from adjacent true paralogues.
(B) The corresponding genomic region on CFA 6 with the distinct genes and their transcriptional orientations indicated by the black pentagons. Below this is the orthologous genomic region from HSA 16 showing five human orthologues (numbered 1–5: ENSG00000005187, ENSG000000166743, ENSG000000166747, ENSG000000066813, and ENSG000000183549). The orthology predictions are indicated with solid black lines. Thus, the dog orthologue for transcript 3 (gene 4) has acquired an extra tandem duplicate (gene 3). Only fragmentary exons on dog CFA6, corresponding to a pseudogene (marked with a cross), can be found for human gene 2, which, therefore, is assigned as an orphan. The human orthologue for the dog gene for transcript 2 unusually appears to have been translocated to HSA 12, as corroborated by BLASTZ [64] genome alignments. Apart from this, gene order and strand have been conserved among orthologues of both lineages, including those for an unrelated orthologue pair (hollow triangles) in the middle of the paralogue cluster (ENSCAFG00000017985 and ENSG000000066654).