paralogon

Paralogon is a term used in comparative genomics to describe a set of chromosomal regions within a single genome that originated from duplication of an ancestral chromosomal segment and that retain a similar gene content and, in some cases, gene order (synteny). Paralogons arise through duplication events that generate paralogous genes and gene blocks, such as segmental duplications or whole-genome duplications, followed by rearrangements, gene loss, and diversification. The presence of multiple paralogons on different chromosomes or distant regions supports the idea that ancient duplication events contributed to genome evolution.

Paralogons are identified by comparative genomics approaches that look for conserved gene content and order across blocks, often enabling reconstruction of ancestral chromosomes. They typically contain families of paralogous genes that are co-located, and the relative order of highly conserved gene families is preserved more than would be expected by chance.

Paralogons have been especially informative in vertebrate genomics, where the hypothesis of early whole-genome duplications (the 2R model) is supported by the existence of multiple paralogous chromosomal regions containing similar sets of genes. They are also observed in plants and other lineages where polyploidy and segmental duplications have shaped genome structure. While paralogons provide evidence for ancient duplications, extensive genome rearrangements and gene loss since the duplication can blur original relationships, complicating reconstruction of ancestral karyotypes.