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Transposable elements (TE) induce structural and epigenetic alterations in their host genome, with major evolutionary implications. These alterations are examined here in the context of allopolyploid speciation, on the recently formed invasive species Spartina anglica, which represents an excellent model to contrast plant genome dynamics following hybridization and genome doubling in natural conditions. Methyl-sensitive transposon display was used to investigate the structural and epigenetic dynamics of TE insertion sites for several elements, and to contrast it with comparable genome-wide methyl-sensitive amplified polymorphism analyses. While no transposition burst was detected, we found evidence of major structural and CpG methylation changes in the vicinity of TE insertions accompanying hybridization, and to a lesser extent, genome doubling. Genomic alteration appeared preferentially in the maternal subgenome, and the environment of TEs was specifically affected by large maternal-specific methylation changes, demonstrating that TEs fuel epigenetic alterations at the merging of diverged genomes. Such genome changes indicate that nuclear incompatibilities in Spartina trigger immediate alterations, which are TE-specific with an important epigenetic component. Since most of this reorganization is conserved after genome doubling that produced a fertile invasive species, TEs certainly play a central role in the shock-induced dynamics of the genome during allopolyploid speciation.

The role played by whole-genome duplication (WGD) in evolution and adaptation is particularly well illustrated in allopolyploids, where WGD is concomitant with interspecific hybridization. This Genome Shock', usually accompanied by structural and functional modifications, has been associated with the activation of transposable elements (TEs). However, the impact of allopolyploidy on TEs has been studied in only a few polyploid species, and not in Brassica, which has been marked by recurrent polyploidy events. Here, we developed sequence-specific amplification polymorphism (SSAP) markers for three contrasting TEs, and compared profiles between resynthesized Brassica napus allotetraploids and their diploid Brassica progenitors. To evaluate restructuring at TE insertion sites, we scored changes in SSAP profiles and analysed a large set of differentially amplified SSAP bands. No massive structural changes associated with the three TEs surveyed were detected. However, several transposition events, specific to the youngest TE originating from the B.oleracea genome, were identified. Our study supports the hypothesis that TE responses to allopolyploidy are highly specific. The changes observed in SSAP profiles lead us to hypothesize that they may partly result from changes in DNA methylation, questioning the role of epigenetics during the formation of a new allopolyploid genome.

• Polyploids can be produced by the union of unreduced gametes or through somatic doubling of F1 interspecific hybrids. The first route is suspected to produce allopolyploid species under natural conditions, whereas experimental data have only been thoroughly gathered for the latter. • We analyzed the meiotic behavior of an F1 interspecific hybrid (by crossing Brassica oleracea and B. rapa, progenitors of B. napus) and the extent to which recombined homoeologous chromosomes were transmitted to its progeny. These results were then compared with results obtained for a plant generated by somatic doubling of this F1 hybrid (CD.S0) and an amphidiploid (UG.S0) formed via a pathway involving unreduced gametes; we studied the impact of this method of polyploid formation on subsequent generations. • This study revealed that meiosis of the F1 interspecific hybrid generated more gametes with recombined chromosomes than did meiosis of the plant produced by somatic doubling, although the size of these translocations was smaller. In the progeny of the UG.S0 plant, there was an unexpected increase in the frequency at which the C1 chromosome was replaced by the A1 chromosome. • We conclude that polyploid formation pathways differ in their genetic outcome. Our study opens up perspectives for the understanding of polyploid origins.

The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents. In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted. Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34 820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploid Triticum turgidum as the genome progenitor. Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids.

The dynamics of genome modification that occurred from the initial hybridization event to the stabilization of allopolyploid species remains largely unexplored. Here, we studied inheritance and expression of rDNA loci in the initial generations of Brassica napus allotetraploids (2n = 38, AACC) resynthesized from Brassica oleracea (2n = 18, CC) and B. rapa (2n = 20, AA) and compared the patterns to natural forms. Starting already from F1 generation, there was a strong uniparental silencing of B. oleracea genes. The epigenetic reprogramming was accompanied with immediate condensation of C-genome nucleolar organizer region (NOR) and progressive transgeneration hypermethylation of polymerase I promoters, mainly at CG sites. No such changes were observed in the A-genome NORs. Locus loss and gains affecting mainly non-NOR loci after the first allotetraploid meiosis did not influence established functional status of NORs. Collectively, epigenetic and genetic modifications in synthetic lines resemble events that accompanied formation of natural allopolyploid species.

Polyploidy (whole-genome duplication) has played a pervasive role in the evolution of fungi and animals, and is particularly prominent in plants (Wendel & Doyle, 2005; Cui et al., 2006; Otto, 2007; Wood et al., 2009). This important evolutionary phenomenon has attracted renewed and growing interest from the scientific community in the last decade since it was discovered that even the smallest plant genomes considered to be ‘diploid' (e.g. Arabidopsis thaliana, reviewed in Henry et al., 2006) have incurred at least one round of whole-genome duplication, possibly predating the origins of the angiosperms (Soltis et al., 2009). Polyploidy is an important speciation mechanism for all eukaryotes and has profound impacts on biodiversity dynamics and ecosystem functioning. Newly formed polyploids, and particularly those of hybrid origin (allopolyploids), frequently exhibit rapid range expansion (Ainouche et al., 2009), and over long periods of evolutionary time, polyploidy has increased morphological complexity and probably reduced the risk of species extinction (Fawcett et al., 2009). Last, but not least, genome duplication has often provided the raw material for plant domestication (e.g. wheat, Dubkovsky & Dvorak, 2007) and thus has had a major impact on human societies and the development of an agrarian lifestyle.

• Transposable elements (TE) induce structural and epigenetic alterations in their host genome, with major evolutionary implications. These alterations are examined here in the context of allopolyploid speciation, on the recently formed invasive species Spartina anglica, which represents an excellent model to contrast plant genome dynamics following hybridization and genome doubling in natural conditions. • Methyl-sensitive transposon display was used to investigate the structural and epigenetic dynamics of TE insertion sites for several elements, and to contrast it with comparable genome-wide methyl-sensitive amplified polymorphism analyses. • While no transposition burst was detected, we found evidence of major structural and CpG methylation changes in the vicinity of TE insertions accompanying hybridization, and to a lesser extent, genome doubling. Genomic alteration appeared preferentially in the maternal subgenome, and the environment of TEs was specifically affected by large maternal-specific methylation changes, demonstrating that TEs fuel epigenetic alterations at the merging of diverged genomes. • Such genome changes indicate that nuclear incompatibilities in Spartina trigger immediate alterations, which are TE-specific with an important epigenetic component. Since most of this reorganization is conserved after genome doubling that produced a fertile invasive species, TEs certainly play a central role in the shockinduced dynamics of the genome during allopolyploid speciation.

In this paper, we examine how the Spartina system has helped our understanding of the genomic aspects of allopolyploid speciation in the context of biological invasion. More specifically the respective roles of hybridization and genome duplication in the success of newly formed allopolyploid species are explored. Hybridization appears to have triggered genetic and epigenetic changes in the two recently formed European homoploid hybrids S. x towsendii and S. x neyrautii. Deviation from parental structural additivity is observed in both hybrids, with different patterns when considering transposable element insertions or AFLP and methylation alteration. No important changes are observed in the invasive allopolyploid Spartina anglica that inherited the identical genome to S. x townsendii. The repeated rRNA genes are not homogenized in the allopolyploid, and both parental repeats are expressed in the populations examined. Transcriptomic changes suggest possible gene silencing in both hybrids and allopolyploid. In the long-term of evolutionary time, older hexaploid Spartina species (Spartina alterniflora, Spartina maritima and Spartina foliosa) appear to have selectively retained differential homeologous copies of nuclear genes. Waxy gene genealogies suggest a hybrid (allopolyploid) origin of this hexaploid lineage of Spartina. Finally, nuclear and chloroplast DNA data indicate a reticulate origin (alloheptaploid) of the invasive Spartina densiflora. All together these studies stress hybridization as a primary stimulus in the invasive success of polyploid Spartina species.