Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species

Abstract

Transposable elements (TEs) are widely distributed repetitive sequences in the genomes across the tree of life, and represent an important source of genetic variability. Their distribution among genomes is specific to each lineage. A phenomenon associated with this feature is the sudden expansion of one or several TE families, called bursts of transposition. We previously proposed that bursts of the Mariner family (DNA transposons) contributed to the speciation of Rhodnius prolixus Stål, 1859. This hypothesis motivated us to study two additional species of the R. prolixus complex: Rhodnius montenegrensis da Rosa et al., 2012 and Rhodnius marabaensis Souza et al., 2016, together with a new, de novo annotation of the R. prolixus repeatome using unassembled short reads. Our analysis reveals that the total amount of TEs present in Rhodnius genomes (19% to 23.5%) is three to four times higher than that expected based on the original quantifications performed for the original genome description of R. prolixus. We confirm here that the repeatome of the three species is dominated by Class II elements of the superfamily Tc1-Mariner, as well as members of the LINE order (Class I). In addition to R. prolixus, we also identified a recent burst of transposition of the Mariner family in R. montenegrensis and R. marabaensis, suggesting that this phenomenon may not be exclusive to R. prolixus. Rather, we hypothesize that whilst the expansion of Mariner elements may have contributed to the diversification of the R. prolixus-R. robustus species complex, the distinct ecological characteristics of these new species did not drive the general evolutionary trajectories of these TEs.

Historical Biogeography and the Evolution of Hematophagy in Rhodniini (Heteroptera: Reduviidae: Triatominae)

“…The unique specimen was found very damaged in Sergipe state, Brazil, a region included in the distribution range of R. domesticus, therefore, examination of further material is essential to confirm whether or not R. zeledoni is a valid species. Following Monteiro et al (2018), R. marabaensis dos Santos Souza et al, 2016 has been suggested to be a genetic variant very close to R. robustus Larrousse, 1927 (specific status recently considered valid by Castro et al, 2020) and R. taquarussuensis (Rosa et al, 2017), was synonymized with R. neglectus Lent, 1954by Nascimento et al (2019 based on interspecific crosses and molecular markers.…”

Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species

“…According to the annotation of this genome assembly, the repeatome of R. prolixus —repeated DNA sequences composing a genome [ 3 ]—make up to 5.6% of the genome, with Class II transposable elements being the main components [ 1 ]. Recently, Castro et al [ 4 ] applied dnaPipeTE software [ 5 ] to re-evaluate the transposable element (TEs) quantification in the R. prolixus genome, with astonishing results. Using the same raw data obtained in the genome assembly project, Castro et al [ 4 ] estimated that the amount of TEs in the R. prolixus genome ranged between 19% and 23%, that is, three to four times higher than the original quantification of Mesquita et al [ 1 ].…”

“…Recently, Castro et al [ 4 ] applied dnaPipeTE software [ 5 ] to re-evaluate the transposable element (TEs) quantification in the R. prolixus genome, with astonishing results. Using the same raw data obtained in the genome assembly project, Castro et al [ 4 ] estimated that the amount of TEs in the R. prolixus genome ranged between 19% and 23%, that is, three to four times higher than the original quantification of Mesquita et al [ 1 ]. In addition, they evaluated other sibling species, R. montenegrensis and R. marabaensis (formerly R. robustus II and III, respectively [ 6 ]), with similar results.…”

Taxonomy, Evolution, and Biogeography of the Rhodniini Tribe (Hemiptera: Reduviidae)

“…In this study, it was concluded that R. montenegrensis and R. robustus clade II are in all likelihood the same species [127]. However, the repeatome and proteomic analyses detected high differentiation between R. prolixus, R. montenegrensis, and R. marabaensis, showing they are different species [144,145].…”