[show abstract][hide abstract] ABSTRACT: The genomes of most Nicotiana species contain three different subfamilies of the Tnt1 retrotransposon, which differ completely in their U3 sequence, whereas the rest of the sequence is relatively constant. The results presented here show that all three Tnt1 subfamilies are expressed in tobacco (Nicotiana tabacum) and that the U3 sequence variability correlates with differences in the pattern of expression of the Tnt1 elements. Each of the three Tnt1 subfamilies is induced by stress, but their promoters have a different response to different stress-associated signaling molecules. The Tnt1A subfamily is particularly strongly induced by elicitors and methyl jasmonate, whereas expression of the Tnt1C subfamily is more sensitive to salicylic acid and auxins. The direct relationship between U3 sequence variability and differences in the stress-associated expression of the Tnt1 elements present in a single host species gives support to our model that postulates that retrotransposons have adapted to their host genomes through the evolution of highly regulated promoters that mimic those of the stress-induced plant genes. Moreover, here we show that the analysis of the transcriptional control of a retrotransposon population such as Tnt1 provides new insights into the study of the complex and still poorly understood network of defense- and stress-induced plant signal transduction pathways.