Impact of transposable elements on the organization and function of allopolyploid genomes

Abstract

Summary Transposable elements (TEs) represent an important fraction of plant genomes and are likely to play a pivotal role in fuelling genome reorganization and functional changes following allopolyploidization. Various processes associated with allopolyploidy (i.e. genetic redundancy, bottlenecks during the formation of allopolyploids or genome shock following genome merging) may allow accumulation of TE insertions. Our objective in carrying out a survey of the literature and a comparative analysis across different allopolyploid systems is to shed light on the structural, epigenetic and functional modifications driven by TEs during allopolyploidization and subsequent diploidization. The available evidence indicates that TE proliferation in the short or the long term after allopolyploidization may be restricted to a few TEs, in specific polyploid systems. By contrast, data indicate major structural changes in the TE genome fraction immediately after allopolyploidization, mainly through losses of TE sequences as a result of recombination. Emerging evidence also suggests that TEs are targeted by substantial epigenetic changes, which may impact gene expression and genome stability. Furthermore, TEs may directly or indirectly support the evolution of new functionalities in allopolyploids during diploidization. All data stress allopolyploidization as a shock associated with drastic genome reorganization. Mechanisms controlling TEs during allopolyploidization as well as their impact on diploidization are discussed.

Organization and evolution of transposable elements along the bread wheat chromosome 3B

“…In contrast to other grass genomes where TEs have mainly transposed recently, we found a major amplification period 1.5 MYA that has been followed by a period of silencing and/or of increased loss from 1.0 MYA until now, confirming that the two hybridization events that led to hexaploid wheat did not trigger massive activation of transposition. Previous studies in wheat have shown a TE transposition burst immediately after allopolyploidization [36,52], but as suggest by Parisod et al [53], this is probably a phenomenon restricted to specific TE families, and to mostly young, active TE populations. The availability of 21,165 complete LTR-RTs allowed us to study the TE activity at a scale not reached so far, revealing that each family had its own period of activity.…”

Genome reorganization in F 1 hybrids uncovers the role of retrotransposons in reproductive isolation

“…Several lines of evidence connect early hybridizationinduced genome changes with bursts of TE instability (reviewed in [16]). Thousands of interspersed copies of fastevolving repetitive sequences such as long terminal repeat retrotransposons (LTR-RTs; for a recent review, see [17]) may indeed be activated by interspecific hybridization (i.e.…”

“…Under the genome shock model, the merging of parental LTR-RTs displaying divergence in copy numbers and/or in nucleotide composition results in quantitative and qualitative imbalance between nuclear copies and maternally transmitted cytoplasmic small interfering RNAs (siRNA), leading to their immediate derepression [18][19][20]. Following such new interactions, only conflicting LTR-RTs are expectedly activated [16,21], with probable deleterious consequences for the zygote and/or the endosperm (e.g. hybrid dysgenesis [9,22]).…”

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

“…Once stabilized, young allopolyploids can become successful species (Abbott et al, 2013). The advantage of duplicated genes and chromosomes in the nucleus is, however, not obvious in the short term because genome duplication is frequently associated with various problems, including genomic instability, transposon activation (Parisod et al, 2010), meiotic irregularities (Grandont et al, 2013) and expression imbalance (Adams and Wendel, 2005). One of the manifestations of genomic instability is homeologue loss, which is observed in many natural and synthetic allopolyploids Renny-Byfield and Wendel, 2014).…”