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

Abstract

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...

Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists

“…We cannot discard the possibility that genome assembly issues impaired us from finding complete copies of Merlin in B. saltans and Perkinsela sp. Recently, we have detected complete copies of VIPER retrotransposons in two Trypanosoma cruzi Dm28c assemblies sequenced by PacBio that were missed in 454-based assemblies [59]. The former technology generates long reads and thus allows better quality assembly of the repetitive sequences, which is not yet available for B. saltans and Perkinsela sp.…”

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

“…The DIRS elements were named in recognition of the first retrotransposon containing YR to be described, DIRS-1 , which was found in the slime mold Dictyostelium discoideum (Cappello et al 1985). This order can be divided into four superfamilies based on sequence structure and phylogeny: DIRS-like, Ngaro-like, PATlike , and VIPER-like (Ribeiro et al 2019). In general, the DIRS elements have three open reading frames (ORFs).…”

“…The PAT-like elements are phylogenetically closely related to the DIRS-like elements (Goodwin and Poulter 2001; Goodwin and Poulter 2004; Poulter and Goodwin 2005), although these two groups are not always monophyletic (Ribeiro et al 2019), and they can be differentiated by structural differences in the terminal repeats. Such as for Ngaro-like, PAT-like elements are composed of SDRs (Poulter and Goodwin 2005; Ribeiro et al 2019). The VIPER-like elements also have SDRs, and form a distinct group of retrotransposons restricted to the protozoans of the order Kinetoplastida (Ribeiro et al 2019).…”

“…The copyright holder for this preprint this version posted August 9, 2021. ; https://doi.org/10.1101/2021.08.05.455354 doi: bioRxiv preprint 5 like, and VIPER-like (Ribeiro et al 2019). In general, the DIRS elements have three open reading frames (ORFs).…”

“…The PAT-like elements are phylogenetically closely related to the DIRS-like elements (Goodwin and Poulter 2001;, although these two groups are not always monophyletic (Ribeiro et al 2019), and they can be differentiated by structural differences in the terminal repeats. Such as for Ngaro-like, PAT-like elements are composed of SDRs (which was not certified by peer review) is the author/funder.…”