Genome evolution of allopolyploids: a process of cytological and genetic diploidization

Abstract

Allopolyploidy is a prominent mode of speciation in higher plants. Due to the coexistence of closely related genomes, a successful allopolyploid must have the ability to invoke and maintain diploid-like behavior, both cytologically and genetically. Recent studies on natural and synthetic allopolyploids have raised many discrepancies. Most species have displayed non-Mendelian behavior in the allopolyploids, but others have not. Some species have demonstrated rapid genome changes following allopolyploid formation, while others have conserved progenitor genomes. Some have displayed directed, non-random genome changes, whereas others have shown random changes. Some of the genomic changes have appeared in the F₁ hybrids, which have been attributed to the union of gametes from different progenitors, while other changes have occurred during or after genome doubling. Although these observations provide significant novel insights into the evolution of allopolyploids, the overall mechanisms of the event are still elusive. It appears that both genetic and epigenetic operations are involved in the diploidization process of allopolyploids. Overall, genetic and epigenetic variations are often associated with the activities of repetitive sequences and transposon elements. Specifically, genomic sequence elimination and chromosome rearrangement are probably the major forces guiding cytological diploidization. Gene non-functionalization, sub-functionalization, neo-functionalization, as well as other kinds of epigenetic modifications, are likely the leading factors promoting genetic diploidization.

Does polyploidy occur in central European species of the family Sphaeriidae (Mollusca: Bivalvia)?

“…Many examples of clades that have diverged from a common polyploid ancestor by genome rearrangements are known in various organisms, especially in angiosperms (see [23,24] for references). Lee and O´Foighil [9] proposed this mechanism as the most probable scenario for phylogeny of the North American Sphaerium-Musculium clade.…”

Protoplast fusion in the genus Gentiana: genomic composition and genetic stability of somatic hybrids between Gentiana kurroo Royle and G. cruciata L.

“…Genome rearrangements accompanying sexual hybridization and formation of allopolyploids have been repeatedly described in detail (Comai 2000;Ma and Gustafson 2005;Gao et al 2011). It seems obvious that similar mechanisms must occur during somatic hybridization, but that they can be intensified by specific conditions of protoplast isolation, pretreatment and fusion, as well as further in vitro culture and, especially, a long-term callus phase, which often precedes plant regeneration.…”

The shock of being united and symphiliosis

“…The phenotypic diversity of allopolyploid plants reflects their genomic and epigenetic plasticity, 35 whose scale and variety is reminiscent of that observed in cancer.…”

“…18 Like genomic aberrations in cancer, genomic rearrangements in allopolyploids can range from simple to highly complex, persist through generations, or re-emerge after being in remission for generations. 18,[34][35][36]39 However substantial the genomic restructuring is, "by far, the most striking change to regulation of gene expression in allopolyploids… is that of epigenetic modification". 40 Some of these modifications are also similar to those found in cancers and include genome-wide alterations in cytosine methylation, gene silencing or activation, alteration of gene imprinting, gene non-functionalization, subfunctionalization, neo-functionalization, changes in mRNA splicing and in gene expression.…”

“…40 Some of these modifications are also similar to those found in cancers and include genome-wide alterations in cytosine methylation, gene silencing or activation, alteration of gene imprinting, gene non-functionalization, subfunctionalization, neo-functionalization, changes in mRNA splicing and in gene expression. 30,35,41 Of particular interest are emergent, or so-called non-additive patterns of gene expression, as they can result in new, potentially advantageous phenotypes. 29,[40][41][42] To begin explaining how allopolyploidy causes genomic and epigenetic changes, Barbara McClintock suggested that uniting two distinct genomes in one nucleus is a type of stress, which she named "genomic shock", that triggers restructuring and integration of the parental genomes, 36 but what this stress is, how it is sensed, and how this information is translated into genome restructuring is still unknown.…”