Abstract
Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early stages of allopolyploid stabilization. Homoeologous exchanges (HEs) have been reported in young allopolyploids from across the angiosperms. Although all lineages undergo karyotype change via chromosome rearrangements over time, the early generations after allopolyploid formation are predicted to show an accelerated rate of genomic change. HEs can also cause changes in allele dosage, genome-wide methylation patterns, and downstream phenotypes, and can hence be responsible for speciation and genome stabilization events. Additionally, we propose that fixation of duplication – deletion events resulting from HEs could lead to the production of genomes which appear to be a mix of autopolyploid and allopolyploid segments, sometimes termed “segmental allopolyploids.” We discuss the implications of these findings for our understanding of the relationship between genome instability in novel polyploids and genome evolution.
Highlights
Recent technological advances have vastly expanded access to genomic information, even for complex genomes
We provide an overview of the cytogenetic processes associated with polyploidy, the early stages of polyploid formation, and how these processes may induce genomic structural variation and give rise to novel phenotypes, providing an evolutionary
We have attempted to provide a synopsis of our growing recognition that homoeologous exchange following polyploidy is a common evolutionary process leading to genomically variable progeny that can serve as substrates for natural selection
Summary
Recent technological advances have vastly expanded access to genomic information, even for complex genomes (reviewed by Yuan et al, 2017). In addition to auto- and allo-, Stebbins (1947) proposed a new category of polyploids, known as “segmental” allopolyploids Stebbins used both chromosome behavior and genome structural divergence concepts in his application of the term, as at the time chromosome pairing was thought to rely solely on “structure,” rather than sequence homology. He first mentions that “Cytologically, [segmental allopolyploids] are characterized by the presence of multivalents in varying numbers, so that in meiosis they often resemble autopolyploids more than true allopolyploids.”. It seems important to distinguish mode of formation and evolved meiotic behavior
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