<i>TARE1</i>, a Mutated <i>Copia</i>-Like LTR Retrotransposon Followed by Recent Massive Amplification in Tomato

<div><p>Long terminal repeat retrotransposons (LTR-RTs) are the major DNA components in flowering plants. Most LTR-RTs contain dinucleotides ‘TG’ and ‘CA’ at the ends of the two LTRs. Here we report the structure, evolution, and propensity of a <u>t</u>omato <u>a</u>typical <u>r</u>etrotransposon <u>e</u>lement (<i>TARE1</i>) with both LTRs starting as ‘TA’. This family is also characterized by high copy numbers (354 copies), short LTR size (194 bp), extremely low ratio of solo LTRs to intact elements (0.05∶1), recent insertion (most within 0.75∼1.75 million years, Mys), and enrichment in pericentromeric region. The majority (83%) of the <i>TARE1</i> elements are shared between <i>S. lycopersicum</i> and its wild relative <i>S. pimpinellifolium</i>, but none of them are found in potato. In the present study, we used shared LTR-RTs as molecular markers and estimated the divergence time between <i>S. lycopersicum</i> and <i>S. pimpinellifolium</i> to be <0.5 Mys. Phylogenetic analysis showed that the <i>TARE1</i> elements, together with two closely related families, <i>TARE2</i> and <i>TGRE1</i>, have formed a sub-lineage belonging to a <i>Copia</i>-like <i>Ale</i> lineage. Although <i>TARE1</i> and <i>TARE2</i> shared similar structural characteristics, the timing, scale, and activity of their amplification were found to be substantially different. We further propose a model wherein a single mutation from ‘G’ to ‘A’ in 3′ LTR followed by amplification is responsible for the origin of <i>TARE1</i>, thus providing evidence that the proliferation of a spontaneous mutation can be mediated by the amplification of LTR-RTs at the level of RNA.</p>