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Open AccessArticle

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

1
UNESP—Univ. Estadual Paulista, Departamento de Biologia, São José do Rio Preto, SP 15054-000, Brazil
2
Department of Molecular Biology and Genetics, 107 Biotechnology Building, Cornell University, Ithaca, New York, NY 14853, USA
3
Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
4
Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, F-69622 Villeurbanne, France
*
Author to whom correspondence should be addressed.
These authors contributed equally as first authors.
Genes 2020, 11(2), 170; https://doi.org/10.3390/genes11020170
Received: 20 January 2020 / Accepted: 30 January 2020 / Published: 6 February 2020
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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. View Full-Text
Keywords: repeatome; Mariner family; burst of transposition; dnaPipeTE; Rhodnius prolixus; Rhodnius montenegrensis; Rhodnius marabaensis repeatome; Mariner family; burst of transposition; dnaPipeTE; Rhodnius prolixus; Rhodnius montenegrensis; Rhodnius marabaensis
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Castro, M.R.J.; Goubert, C.; Monteiro, F.A.; Vieira, C.; Carareto, C.M.A. Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species. Genes 2020, 11, 170.

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