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

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...

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Autores principales: Castro, Marcelo R. J., Goubert, Clément, Monteiro, Fernando A., Vieira, Cristina, Carareto, Claudia M. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073582/
https://www.ncbi.nlm.nih.gov/pubmed/32041215
http://dx.doi.org/10.3390/genes11020170
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author Castro, Marcelo R. J.
Goubert, Clément
Monteiro, Fernando A.
Vieira, Cristina
Carareto, Claudia M. A.
author_facet Castro, Marcelo R. J.
Goubert, Clément
Monteiro, Fernando A.
Vieira, Cristina
Carareto, Claudia M. A.
author_sort Castro, Marcelo R. J.
collection PubMed
description 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.
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spelling pubmed-70735822020-03-20 Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species Castro, Marcelo R. J. Goubert, Clément Monteiro, Fernando A. Vieira, Cristina Carareto, Claudia M. A. Genes (Basel) Article 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. MDPI 2020-02-06 /pmc/articles/PMC7073582/ /pubmed/32041215 http://dx.doi.org/10.3390/genes11020170 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Castro, Marcelo R. J.
Goubert, Clément
Monteiro, Fernando A.
Vieira, Cristina
Carareto, Claudia M. A.
Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
title Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
title_full Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
title_fullStr Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
title_full_unstemmed Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
title_short Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
title_sort homology-free detection of transposable elements unveils their dynamics in three ecologically distinct rhodnius species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073582/
https://www.ncbi.nlm.nih.gov/pubmed/32041215
http://dx.doi.org/10.3390/genes11020170
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