Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes
(A) Dotplot displays of the genomic distribution of the mouse orthologs (crosses) of the human ALDH1A-neighbor genes within a 10 Mb-window of the human ALDH1A gene (red: ALDH1A1-neighbor genes; blue: ALDH1A2-neighbor genes; green: ALDH13-neighbor genes; and yellow: ALDH1A3-ogm-neighbor genes), and reveals the presence of four regions (colored boxes) in Mmu7, Mmu9, Mmu13 and Mmu19 orthologous to the human ALDH1A genomic neighborhoods (GN). Mouse chromosomes are represented in the y-axis, and chromosome position is in the x-axis. Table S2 provides gene accession numbers and genomic information for each orthology group represented in the dotplot. (B) A circle-plot shows the pattern of syntenic correspondence between the human ALDH1A GNs (black arcs outside chromosomes) and the candidate mouse orthologous ALDH1A-related chromosomes revealed in A. Figure S2 provide high resolution images of pair-wise gene clusters identified in the orthologous syntenic database  showing orthologous regions of high syntenic conservation between the human and mouse Aldh1a GNs shown in A and B. The correspondence of ALDH1A3 GNs in Hsa 15 and Mmu7 (green lines), and ALDH1A3-ogm GNs in Hsa5 and Mmu13 (golden) strongly supports the conclusion that ALDH1A3 in human is an ortholog, not a paralog, of Aldh1a3 in mouse. These results show that the loss of ALDH1A3-ogm predated the divergence of mouse and human. Circles represent chromosome centromeres.