Abstract
Retrotransposons containing long terminal repeats (LTRs) form a substantial fraction of eukaryotic genomes. The timing of past transposition can be estimated by quantifying the accumulation of mutations in initially identical LTRs. This way, retrotransposons are divided into young, potentially mobile elements, and old that moved thousands or even millions of years ago. Both types are found within a single retrotransposon family and it is assumed that the old members will remain immobile and degenerate further. Here, we provide evidence in Arabidopsis that old members enter into replication/transposition cycles through high rates of intra-family recombination. The recombination occurs pairwise, resembling the formation of recombinant retroviruses. Thus, each transposition burst generates a novel progeny population of chromosomally integrated LTR retrotransposons consisting of pairwise recombination products produced in a process comparable the sexual exchange of genetic information. Our observations provide an explanation for the reported high rates of sequence diversification in retrotransposons.
Highlights
Retrotransposons containing long terminal repeats (LTRs) form a substantial fraction of eukaryotic genomes
Subsequent reverse transcription involves two transfers of DNA strands that lead to the synthesis of a complete copy of a retrotransposon as extrachromosomal DNA terminated by two identical LTRs (Supplementary Fig. 1)
We examined the composition of perfect-matching pair reads in which the sequence of one mate starts exactly at the beginning of the LTR, which is diagnostic of linear extrachromosomal DNA (ecDNA)
Summary
Retrotransposons containing long terminal repeats (LTRs) form a substantial fraction of eukaryotic genomes. The differences in the sequences of initially identical LTRs can be used to estimate the time of the last transposition event[3] Using this notation, young family members that transposed recently are considered to be potentially active and old members to represent historic transposition events. In contrast to the welldocumented formation of recombinant strains during retroviral mix-infections[5], the genetic consequences of the transposition bursts of an entire family of LTR retroelements, consisting of young and old members, are unknown. We examined such consequences using an experimentally induced retrotransposition burst of the endogenous, heat stress-activated family of Arabidopsis LTR retrotransposons Copia[78] or Onsen[6]
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