Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids

Abstract

SummaryThe 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.

Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon

“…For example, it is well established that the WGD event caused changes in genome structure among salmonids (Lien et al 2011; Phillips et al 2013), although the reasons behind the variation and its effects on paralog creation and preservation are unclear. We hypothesize that transposable elements are involved in LGD events in S. salar ; it has been shown that post-WGD transposable element activity is highly genome specific in Brassica (Sarilar et al 2013). LGD events have been detected in both trout (Berthelot et al 2014) and chinook salmon (Brieuc et al 2014), but their prevalence is unclear.…”

Retrotransposons Represent the Most Labile Fraction for Genomic Rearrangements in Polyploid Plant Species

“…In the natural allopolyploid Spartina anglica , evidence of major changes in CpG methylation in the proximity of retrotransposon insertions were found by sequence-specific amplified polymorphism (SSAP) analysis; however, few new TE insertions were proposed among the retrotransposon families investigated (terminal-repeat retrotransposons in miniature, Cassandra and Wis Copia -like retrotransposons) [Parisod et al, 2009], although some fragment losses were detected immediately after hybridisation [Parisod et al, 2010a]. More recently, a study of Athilalike retrotransposons by SSAP in the synthetic allotetraploids B. napus revealed mostly additive profiles when compared with the diploid parents, and the characterisation of nonadditive SSAP bands indicated that genomic rearrangements had occurred rather than new transposition events [Sarilar et al, 2013]. Similar analyses revealed a proliferation of the Tnt 1 retrotransposon after genome doubling in the synthetic Nicotiana tabacum .…”

Genetic analysis of artificial Triticinae amphidiploid Aurotica based on the glaucousness trait

“…The simultaneous mutation in two different genes cannot be explained from the position of random mutagenesis. Over the past 10 to 15 years, a number of literature sources have proven that plant genomes whose origin is associated with allopolyploidization or wide hybridization are prone to some processes that could be interpreted as destabilization of such genomes [24,25,27]. On the phenotypic level, this means the emergence of new traits which were not present in the parent lines [39], new gene alleles of storage proteins [40,41], and material changes in the gene expression [42,43], right up to gene silencing [44].…”

“…In recent literature, significant attention is given to the processes occurring in natural and artificial amphidiploids during formation of their genomes [21][22][23][24][25][26][27]. It seems that the Aurotica genome, which has an introgressive origin, possesses some process resulting in the mutation of the dominant allele into a recessive one at a rate significantly higher than the known average rate of spontaneous mutation per gene per generation.…”