title: Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats.
abstract: Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting with that, only a few families (BARE1 and Romani) showed proliferation in all polyploids. Overall, TE divergence between progenitors was strongly correlated with the degree of restructuring in polyploid TE fractions. TE families present evolutionary trajectories that are decoupled from genome-wide changes after allopolyploidy and have a pervasive impact on their restructuring.
authors.affiliation: Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
authors.forename: Natacha
authors.initials: N
authors.lastname: Senerchia
authors.affiliation: Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.|Musée et Jardins botaniques cantonaux, Avenue de Cour 14bis, 1007, Lausanne, Switzerland.
authors.forename: François
authors.initials: F
authors.lastname: Felber
authors.affiliation: Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Parisod
mesh_terms: D001483:Base Sequence; D004171:Diploidy; D019143:Evolution, Molecular; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D011123:Polyploidy; D018626:Retroelements / Q000235:genetics*; D013045:Species Specificity; D020079:Terminal Repeat Sequences / Q000235:genetics; D014908:Triticum / Q000235:genetics*
chemical_list: D018626:Retroelements
keywords: Aegilops; genome evolution; genome shock; pivotal-differential genome evolution; sequence-specific amplified polymorphism (SSAP); transposable elements (TEs)