Figure 4

The reconstruction of an ancestral cluster. (a) Detailed comparison of gene content and order is shown for the four clusters included in CLIC #39 (see Table 3), containing genes from the OR1 and OR3 families. A schematic ancestral configuration is shown at the bottom row, with inferred minimal number of genes. Genes are presented as triangles colored by subfamily affiliation (bottom row; yellow for subfamily OR1G). Inferred chromosomal rearrangements relative to the ancestor are specified for each species: circle = insertion, X = deletion, arrow = inversion, broken line with number of genes = tandem duplication. A complex duplication in rodent genomes, involving subfamilies OR3A, OR1P, and OR1A, is marked with a rectangle. This duplication was probably formed via several events, some of which occurred after the split between mouse and rat lineages. The same region had experienced another independent event in the dog genome, in which three genes from subfamilies 1A and 1P were inverted as one unit. Tandem duplication in one end of the rodent clusters forms a series of numerous adjacent highly similar genes from the same subfamily (OR1J). The human and mouse orthologous clusters were studied and compared previously [27], and a complex orthology relationship among the genes was described. (b) A phylogenetic tree of CLIC #39 ORs from which the ancestral cluster gene count can be inferred. The phylogenetic tree was generated with Mega version 3.1 [58] using ME algorithm, and Poisson correction for distance calculation. Protein sequences were aligned with Clustalx [59]. The colors of circles next to the phylogenetic branches indicate species (blue = dog, green = rat, orange = mouse, red = human). OR51D1 serves as an out-group. CLIC, clusters in conservation; OR, olfactory receptor.