The distribution of copia-type retrotransposons and the evolutionary history of tomato and related wild species

Retrotransposons are mobile genetic elements that amplify throughout the genome and may be important contributors of genetic diversity. Their distribution is influenced by element behaviour and host-driven controls. We analysed the distribution of three copia-type retrotransposons, ToRTL1, T135 and Tnt1 using sequence-specific amplification polymorphism in self-compatible (SC) and incompatible (SI) species of Solanum subsection Lycopersicon, and genetically mapped polymorphic insertions in S. lycopersicum (tomato). The majority of polymorphic insertions (61%) are located in centromeric regions of the tomato genome. A significant positive relationship was detected between insertion polymorphisms and mating system, independent of selection as most insertions were found to be neutral. As insertion patterns successfully inferred interspecific relationships of Solanum subsection Lycopersicon, our results suggest that the distribution of ToRTL1, T135 and Tnt1 may essentially be determined by selection removing strongly deleterious insertions, with genetic drift and mating system, but not recombination rate, playing important roles.