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Retrotransposons are distributed in all eukaryotic genomes and are major components of plant genomes. They belong to the class of reverse-transcribing elements that multiply by transferring genetic information from RNA to DNA, like retroviruses and pararetroviruses. Retrotransposons have recently been reclassified according to the viral nomenclature, in orders Retrovirales for LTR retrotransposons and Retrales for non-LTR retrotransposons. LTR retrotransposons are structurally closely related to retroviruses and their amplification cycle mirrors the intracellular step of the retroviral cycle, with strong similarities in the reverse transcription and integration processes. In addition, LTR retrotransposons population structures resemble viral quasispecies, with possibly adaptative optimal patterns of amplification selected in each host genome. Various structural variants are found in plants, with defective versions amplified at surprisingly high level. Depending on the order of the coding domains, LTR retrotransposons are classified in the families Pseudoviridae (Ty1/copia-type) and Metaviridae (Ty3/gypsy-type), with at least two genera per family represented in plants. Additional ORFs displaying structural features of the retroviral env protein have been detected in some elements of both families. Although the involvement of these env-like domains in infectiosity remains highly hypothetical, their recurrent presence in plant elements and the conservation of specific expression mechanisms suggest that they may play an important role in the element's life cycle. |
