Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization

Abstract

Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60-70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families.

Figure 1

Definition of homologous gene quartets and inference of conversion based on phylogenetic topology changes. In (a), arrows show genes with colors reflecting homology. Gene quartets are formed by rice (R) paralogs R1 and R2, and their respective sorghum (S) orthologs S1 and S2. In (b) to (j), squares symbolize a duplication event in the common ancestral genome, and circles symbolize species divergence. The expected phylogenetic relationship of the homologous quartets is displayed in (b) if no conversion has occurred; (c) to (j) show different types of conversion, for example, (c) shows the expected pattern if gene R2 is converted by R1; (d) if gene S1 is converted by S2; and (g) if both the above conversions occurred.

Figure 2

Homology pattern of chromosomes rice chromosomes R11, R12, and their respective sorghum orthologs S5 and S8. Chromosomes are shown with black curved lines, with ovals displaying centromeres. “L” and “S” show long and short arms of the chromosomes. The interior lines show the duplicated genes within genomes and orthologs between genomes. Colors of lines show Ks values (synonymous substitution rates between homologous genes), as illustrated in the right-bottom corner.