Duplicated genes evolve independently after polyploid formation in cotton

Abstract

Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci recently doubled by polyploidy (homoeologues) has not been studied. Here we use locus-specific isolation techniques with comparative mapping to characterize the evolution of homoeologous loci in allopolyploid cotton (Gossypium hirsutum) and in species representing its diploid progenitors. We isolated and sequenced 16 loci from both genomes of the allopolyploid, from both progenitor diploid genomes and appropriate outgroups. Phylogenetic analysis of the resulting 73.5 kb of sequence data demonstrated that for all 16 loci (14.7 kb/genome), the topology expected from organismal history was recovered. In contrast to observations involving repetitive DNAs in cotton, there was no evidence of interaction among duplicated genes in the allopolyploid. Polyploidy was not accompanied by an obvious increase in mutations indicative of pseudogene formation. Additionally, differences in rates of divergence among homoeologues in polyploids and orthologues in diploids were indistinguishable across loci, with significant rate deviation restricted to two putative pseudogenes. Our results indicate that most duplicated genes in allopolyploid cotton evolve independently of each other and at the same rate as those of their diploid progenitors. These indications of genic stasis accompanying polyploidization provide a sharp contrast to recent examples of rapid genomic evolution in allopolyploids.

Figure 1

Null hypothesis for sequence evolution in allopolyploids. (A) Phylogenetic history of diploid (A- and D-genome) and allopolyploid cotton species, as inferred from multiple lines of evidence (–34). Allopolyploid cottons formed 0.5–2 mya from hybridization between A-genome and D-genome diploids, which diverged from each other ca. 5–10 mya. (B) Phylogenetic expectations of independence and equal rates of sequence evolution following allopolyploid formation. Shown are phylogenetic relationships between sequences from diploid progenitor ge-nomes (A and D) and their orthologous counterparts (A_T and D_T) in derived allopolyploids. G. kirkii serves as the outgroup (32) for testing both rate equivalence and independence. (C) An accelerated rate of sequence evolution in allopolyploids will generate longer branches leading to A_T and/or D_T than to A and D. (D) Concerted evolutionary forces may lead to nonindependent sequence evolution after allopolyploidization. Illustrated is conversion of an A-subgenome homoeologue to a D-subgenomic form, as has been demonstrated for ribosomal genes in allotetraploid Gossypium (20).

Figure 2

Most-parsimonious trees obtained for the evolution of 16 low-copy loci in diploid (A₁, D₅) and allopolyploid (A_T, D_T) Gossypium genomes. The outgroup taxon, G. kirkii, is designated by the abbreviation Gk. Branch lengths (number of inferred changes) are indicated. (Lower Right) Merger of the 16 data sets leads to the global analysis shown.