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Mirabilis jalapa L is the most commonly grown ornamental species of Mirabilis and is available in a range of brilliant colors. However, genetic research on Mirabilis jalapa L is limited. Using fluorescent differential display (FDD) screening, we report the identification of a novel Ty1-copia-like retrotransposon in the genome of the red flower of Mirabilis jalapa L, and we named it REC66 based on its sequence homology to the GAG protein from Ty1-copia retrotransposon. Using degenerate primers based on the DNA sequence of REC66, a total of fourteen different variants in reverse transcriptase (RT) sequence were recovered from the genomic DNA. These RT sequences show a high degree of heterogeneity characterized mainly by deletion mutation; they can be divided into three subfamilies, of which the majority encode defective RT. This is the first report of a Ty1-copia retrotransposon in Mirabilis jalapa L. The finding could be helpful for the development of new molecular markers for genetic studies, particularly on the origin and evolutionary relationships of M. jalapa L, and the study of Ty1-copia retrotransposons and plant genome evolution in the genus Mirabilis or family Nyctaginaceae. [ABSTRACT FROM AUTHOR]