Structural and functional divergence of homoeologous genes in allopolyploid plant genomes

Allopolyploid organisms can be formed by hybridization between closely related plant species with similar genomes. It is believed that many plant species have passed through allopolyploidization, which played a significant role in the formation of a huge diversity of plants, as well as their high adaptive capacity. Thanks to the whole genome sequencing of a wide range of angiosperm species and comparative analysis of genome structure, the sequence of events that formed the genomes of modern plant taxa was restored. These studies have shown that many diploid species have passed through more than one cycle of polyploidization-diploidization. The purpose of this review is to summarize the estimates of what proportion of genes is undergoing changes due to allopoly-ploidization and to illustrate the variety of mechanisms underlying the functional divergence of homoeologous copies (orthologous genes in allopolyploid subgenomes). Changes of individual copies can be associated with epigenetic features of the gene organization (the methylation status of the promoter region or the presence of copy-specific small interfering RNA) or can affect structure of the coding or regulatory regions of the gene. Studies on artificial allopolyploid plants showed widespread transcriptional dominance and change of the transcription level as compared with the genes of diploid parental forms. The study of the transcription of certain homoeologous gene copies allowed estimating the extent of the complete suppression of certain homoeologous genes in newly synthesized (0.4–5.0 %) and natural (30 %) allopolyploids. One the whole, full or partial suppression affects up to 49% of the wheat genes.