Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms

Abstract

Gene duplication is postulated to have played a major role in the evolution of biological novelty. Here, gene duplication is examined across levels of biological organization in an attempt to create a unified picture of the mechanistic process by which gene duplication can have played a role in generating biodiversity. Neofunctionalization and subfunctionalization have been proposed as important processes driving the retention of duplicate genes. These models have foundations in population genetic theory, which is now being refined by explicit consideration of the structural constraints placed upon genes encoding proteins through physical chemistry. Further, such models can be examined in the context of comparative genomics, where an integration of genelevel evolution and species-level evolution allows an assessment of the frequency of duplication and the fate of duplicate genes. This process, of course, is dependent upon the biochemical role that duplicated genes play in biological systems, which is in turn dependent upon the mechanism of duplication: whole genome duplication involving a co-duplication of interacting partners vs. single gene duplication. Lastly, the role that these processes may have played in driving speciation is examined.

Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs

“…Comeron, 2001;Eyre-Walker, 2006 Gu et al, 2002b) and only 2% of genes had ENC levels between 32 and 35, suggesting that synonymous sites in this dataset should conform to neutrality reasonably well. Thus, as has been assumed by others here it was assumed that synonymous site divergence is useful measure for the relative ages of gene duplicate pairs (Kim and Yi, 2006;Wang et al, 2006;Gu and Su, 2007;Guan et al, 2007;Ha et al, 2007;Jiang et al, 2007;Johnston et al, 2007;Roth et al, 2007). (Table 2).…”

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

“…Genome-wide or local gene duplication is crucial for the origin of new gene functions 37 . Microsynteny analysis of the genomic regions surrounding CS in hot pepper (~436 kb) and tomato (~183 kb) identified acyltransferase gene clusters in both species (Fig.…”

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

“…Gene duplication as a means of generating novel genes has been realized for a long time (Haldane 1933;Muller 1935;Bridges 1936;Lewis 1951;Stephens 1951;Nei 1969). Gradual change from a duplicated gene, via those encoding isoforms, up to the acquisition of novel functions including subfunctionalization (Lynch and Force 2000) is now well documented (Roth et al 2007;Kaessmann 2010;Chen et al 2013). Gene amplification can occur via segmental duplication (Bailey and Eichler 2006) or retroposition (Brosius 1999a;Babushok et al 2007) with a lower "success rate" for the latter.…”