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 authori...
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