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Background  Kinetoplastids are a flagellated group of protists, including some parasites, such as  Trypanosoma  and  Leishmania  species, that can cause diseases in humans and other animals. The genomes of these species enclose a fraction of retrotransposons including  VIPER  and  TATE , two poorly studied transposable elements that encode a tyrosine recombinase (YR) and were previously classified as DIRS elements. This study investigated the distribution and evolution of  VIPER  and  TATE  in kinetoplastids to understand the relationships of these elements with other retrotransposons.    Results  We observed that  VIPER  and  TATE  have a discontinuous distribution among Trypanosomatidae, with several events of loss and degeneration occurring during a vertical transfer evolution. We were able to identify the terminal repeats of these elements for the first time, and we showed that these elements are potentially active in some species, including  T. cruzi  copies of  VIPER . We found that  VIPER  and  TATE  are strictly related elements, which were named in this study as  VIPER-like . The reverse transcriptase (RT) tree presented a low resolution, and the origin and relationships among YR groups remain uncertain. Conversely, for RH,  VIPER-like  grouped with  Hepadnavirus , whereas for YR,  VIPER-like  sequences constituted two different clades that are closely allied to  Crypton . Distinct topologies among RT, RH and YR trees suggest ancient rearrangements/exchanges in domains and a modular pattern of evolution with putative independent origins for each ORF.    Conclusions  Due to the presence of both elements in  Bodo saltans,  a nontrypanosomatid species, we suggested that  VIPER  and  TATE  have survived and remained active for more than 400 million years or were reactivated during the evolution of the host species. We did not find clear evidence of independent origins of  VIPER-like  from the other YR retroelements, supporting the maintenance of the DIRS group of retrotransposons. Nevertheless, according to phylogenetic findings and sequence structure obtained by this study and other works, we proposed separating DIRS elements into four subgroups:  DIRS-like, PAT-like, Ngaro-like,  and  VIPER-like.Electronic supplementary material  The online version of this article (10.1186/s13100-019-0175-2) contains supplementary material, which is available to authorized users.

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons