Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity
Retrotransposable elements (RTEs) are highly common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The “copy-out and paste-in” life cycle of replicative transposition in these dispersive and ub
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Introduction All eukaryotic genomes contain DNA sequences termed “repetitive elements” that are present in multiple copies throughout the genome [1–3]. These repetitive sequences can either be tandemly arrayed or interspersed throughout the genome [4]. Interspersed repetitive sequences comprise a large fraction of eukaryotic genomes and are predominantly comprised of retrotransposable elements (retrotransposons, or RTEs) [1, 5–9]. For example, retrotransposons can comprise up to 90% of the genome in some eukaryotes. In most of the species studied thus far, these interspersed repeats are distributed unevenly across the nuclear genome, with some repeats having a tendency to cluster around the centromeres or telomeres [10, 11]. Moreover, RTEs are predominantly located in heterochromatic regions of the genome. Cereals and
Pascale Besse (ed.), Molecular Plant Taxonomy: Methods and Protocols, Methods in Molecular Biology, vol. 2222, https://doi.org/10.1007/978-1-0716-0997-2_15, © Springer Science+Business Media, LLC, part of Springer Nature 2021
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citrus fruits often have retrotransposons locally nested within one another and in extensive domains, referred to as “retrotransposon seas,” which surround gene islands. Nevertheless, the most prevalent retrotransposons are dispersed throughout the genome [3]. RTEs can be subdivided on the basis of their size; short interspersed elements are less than 1000 bp long, and the rest are considered to be long interspersed elements. Variation in the copy number of repeat elements and internal rearrangements on both homologous chromosomes can arise after the induction of recombinational processes during the meiotic prophase [12, 13]. It was previously shown that a specific retrotransposon is universally distributed among closely and distantly related species [14, 15]. Although there is no unique set of retrotransposons for a particular species [14, 16–19], related species have phylogenetically cognate (related) RTE sequences. As such, any high-copy mobile genetic element (MGE) shows phylogenetic similarity among related species. For example, both the long terminal repeats (LTRs) and the central part are conserved, consistent with their parent plant families. Generally, retrotransposons have not been extensively explored as phylogenetic markers, except in a few articles that have discussed the phylogenetic relationships among concrete retrotransposon sequences [14, 15, 17, 20]. Since high-copy RTEs are widely distributed and diverse in eukaryotes, they offer many advantages for their use in eukaryotic phylogenetic studies. Their features of abundance, general dispersion, and activity provide ideal conditions for developing molecular phylogenetic markers [21, 22]. 1.1 LTR Retrotransposons
Transposable elements (TEs) are classified into two main groups in eukaryotic genomes, defined according to their mechanism of transposition [23]. Class I TEs transpose through an RNA intermediate, which class II transposons lack [24] (Fig. 1). The two classes can be f
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