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

Abstract

Understanding how increased genome size and diversity within polyploid genomes impacts plant evolution and breeding continues to be challenging. Although historical studies by McClintock suggested the importance of transposable elements mediated by polyploidisation on genomic changes, data from plant crosses remain scarce. Despite the absence of a conclusive proof regarding autonomous retrotransposon movement in synthetic allopolyploids, the transposition of retrotransposons and their ubiquitous dispersion in all plant species might explain the positive correlation between the genome size of plants and the prevalence of retrotransposons. Here, we address polyploidisation-mediated rearrangements of retrotransposon-associated sequences and discuss a tendency for a preferential restructuring of large ancestral genomes after polyploidisation. A comparative analysis of the frequency of modifications of retrotransposon-associated sequences in synthetic polyploids with marked differences in genome sizes is presented. Such analyses suggest the absence of a significant difference in the rates of rearrangements despite vast dissimilarities in the retrotransposon copy number between species, which emphasises the high plasticity of this genomic feature. See also the sister article focusing on animals by Arkhipova and Rodriguez in this themed issue.

Genetic Diversity Assessment of Portuguese Cultivated Vicia faba L. through IRAP Markers

“…IRAP PCR was performed in a 20 µL reaction mixture as previously described [38], using primers targeting the LTR of retrotransposons Nikita (5 1 -CGCTCCAGCGGTACTGCC) [39], Tat-1 (5 1 -TCCTCGTAAAACAACCACAAG), and Athila4-6 (5 1 -AAATGGATGCTCAAAACATGC) [19]. PCR products were separated by 1.7% agarose gel electrophoresis and detected by Ethidium Bromide staining.…”

“…IRAP methodology was used to target three distinct retrotransposable elements: Nikita (identified in barley [39]), Tat-1 [44] and Athila4-6 [45] (the last two from A. thaliana). These retrotransposons have been previously used to study genome diversity in other species besides the ones where they were identified [19,33,34,46]. They were selected to produce consistent banding profiles with easily distinguishable bands allowing the assessment of faba bean genotypes.…”

Plant Transposable Elements and Their Application to Genetic Analysis via High-throughput Sequencing Platform

“…When first discovered, TEs were considered as selfish or junk DNA, but they are now recognized as key components of genome evolution and diversification, as well as gene regulation (Feschotte and Pritham, 2007;Volff, 2006). TEs constitute a considerable fraction of the eukaryotic genome, and LTR retrotransposons are particularly abundant in higher-plant genomes (Bento et al, 2013;Tenaillon et al, 2010). Wide variations of genome size exist among plant species, and a difference of over 2000-fold has been reported between Genlisea margaretae Hutch.…”

“…Wide variations of genome size exist among plant species, and a difference of over 2000-fold has been reported between Genlisea margaretae Hutch. (63.4 Mbp) and Paris japonica (149,000 Mbp) (Pellicer et al, 2010); these differences are thought to have been driven by factors such as polyploidization and TE amplification (Bento et al, 2013;Tenaillon et al, 2010). In fact, plant genome size and TE (especially retrotransposon) content are well correlated (Tenaillon et al, 2010): plant species with huge genomes, such as maize and barley, tend to have higher proportions of TEs (> 85%), whereas plant species with smaller genomes, such as Arabidopsis thaliana and Brachypodium distachyon, show lower levels (20%-30%).…”

“…In addition, over 75% of the maize genome consists of retrotransposons, whereas DNA transposons occupy only 8.6% of the genome (Schnable et al, 2009). This situation is likely due to the "copy and paste" transposition mechanism of retrotransposons, which increases their copy numbers dramatically and contributes to the expansion of plant genomes (Bento et al, 2013;Kumar and Bennetzen, 1999). Thus, multiple and diverse retrotransposon families with high copy numbers exist in present genomes.…”