Mobilization of retrotransposons in synthetic allotetraploid tobacco

Abstract

Summary• Allopolyploidy is a major driving force in plant evolution and can induce rapid structural changes in the hybrid genome. As major components of plant genomes, transposable elements are involved in these changes. In a previous work, we observed turnover of retrotransposon insertions in natural allotretraploid tobacco (Nicotiana tabacum). Here, we studied the early stages of allopolyploid formation by monitoring changes at retrotransposon insertion sites in the Th37 synthetic tobacco.• We used sequence-specific amplification polymorphism (SSAP) to study insertion patterns of two populations of the Tnt1 retrotransposon in Th37 S4 generation plants, and characterized the nature of polymorphic insertion sites.• We observed significant amplification of young Tnt1 populations. Newly transposed copies were amplified from maternal elements and were highly similar to Tnt1A tobacco copies amplified in response to microbial factors. A high proportion of paternal SSAP bands were not transmitted to the hybrid, corresponding to various rearrangements at paternal insertion sites, including indels or the complete loss of the Tnt1 ⁄ flanking junction.• These data indicate that major changes, such as retrotransposon amplification and molecular restructuring in or around insertion sites, occur rapidly in response to allopolyploidy.

Polyploidy and novelty: Gottlieb's legacy

“…Such a burst in transpositional activity has been proposed in allopolyploids, based on the fact that all genes are duplicated and the genome can therefore tolerate higher levels of TE activity [82]. An increase in the copy number of a Tnt1 retrotransposon was detected in allotetraploid tobacco [83], but no similar transposition burst was detected after genome doubling in the allopolyploid Spartina anglica [84]. In synthesized allohexaploid wheat (T. aestivum), both AFLP-based analysis and small RNA high-throughput sequencing data showed that the abundance of Veju long terminal repeats decreased in allopolyploid wheat and is associated with a decrease in CG methylation [85,86].…”

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

“…DNA is integrating into the nuclear genome from a variety of sources, including (retro)transposable elements, viral DNA, plastid and mitochondrial sequences. Furthermore, stress and polyploidy activate retrotransposon transcription and integration (Grandbastien, 1998;Petit et al, 2010). The inevitable genome enlargement is counteracted by mechanisms which excise DNA (e.g.…”

“…carrying chromosomal translocations, deletions and duplications; Lim et al, 2006;Gaeta et al, 2007). Even in synthetic polyploids, changing copy numbers of repeats can be observed (Petit et al, 2010;Renny-Byfield et al, 2011). From these variants, selection favours the most fertile individuals where chromosome pairing and segregation are regular.…”

“…(Retro)transposon mobility, which can be triggered by both polyploidy and stress (Grandbastien et al, 2005;Petit et al, 2010), is regulated by epigenetic processes. Epigenetic mechanisms are also involved in regulating DNA condensation, which can be predicted to influence the frequency of recombination-based mechanisms that also act to homogenize the genome.…”

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

“…For example, the last polyploidy in the sorghum (Sorghum bicolor) lineage was about 70 million years ago (mya), many millions of years before the origin and broad diversification of the grass family (Paterson et al, 2004). Beyond doubling genome size, polyploidy has been observed to serve as a 'genomic shock' that activates TE amplification and resultant genome rearrangement, possibly through altering the balance in their epigenetic silencing (O'Neill et al, 1998;Ozkan et al, 2001;Madlung et al, 2005;Parisod et al, 2009;Petit et al, 2010). After polyploidy, an eventual diploidization process occurs that leads to exclusive disomic inheritance and the loss of a subset of the genes that were, for instance, doubled in nuclear copy number by a diploid to tetraploid polyploid event.…”