Homology-free detection of transposable elements unveils their dynamics in three ecologically distinct rhodnius species
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3390/genes11020170 http://hdl.handle.net/11449/200057 |
Resumo: | 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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Homology-free detection of transposable elements unveils their dynamics in three ecologically distinct rhodnius speciesBurst of transpositionDnaPipeTEMariner familyRepeatomeRhodnius marabaensisRhodnius montenegrensisRhodnius prolixusTransposable 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.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)UNESP—Univ. Estadual Paulista Departamento de Biologia, São José do Rio PretoDepartment of Molecular Biology and Genetics Cornell University, 107 Biotechnology BuildingLaboratório de Epidemiologia e Sistemática Molecular Instituto Oswaldo Cruz FIOCRUZLaboratoire de Biométrie et Biologie Evolutive Université de Lyon Université Lyon 1 CNRS UMR5558UNESP—Univ. Estadual Paulista Departamento de Biologia, São José do Rio PretoUniversidade Estadual Paulista (Unesp)Cornell UniversityFIOCRUZUMR5558Castro, Marcelo R. J. [UNESP]Goubert, ClémentCarareto, Claudia M. A. [UNESP]Monteiro, Fernando A.Vieira, Cristina2020-12-12T01:56:25Z2020-12-12T01:56:25Z2020-02-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3390/genes11020170Genes, v. 11, n. 2, 2020.2073-4425http://hdl.handle.net/11449/20005710.3390/genes110201702-s2.0-8507923635934257729983192160000-0002-0298-1354Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenesinfo:eu-repo/semantics/openAccess2021-11-05T12:48:06Zoai:repositorio.unesp.br:11449/200057Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:05:12.932512Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
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 |
spellingShingle |
Homology-free detection of transposable elements unveils their dynamics in three ecologically distinct rhodnius species Castro, Marcelo R. J. [UNESP] Burst of transposition DnaPipeTE Mariner family Repeatome Rhodnius marabaensis Rhodnius montenegrensis Rhodnius prolixus |
title_short |
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_sort |
Homology-free detection of transposable elements unveils their dynamics in three ecologically distinct rhodnius species |
author |
Castro, Marcelo R. J. [UNESP] |
author_facet |
Castro, Marcelo R. J. [UNESP] Goubert, Clément Carareto, Claudia M. A. [UNESP] Monteiro, Fernando A. Vieira, Cristina |
author_role |
author |
author2 |
Goubert, Clément Carareto, Claudia M. A. [UNESP] Monteiro, Fernando A. Vieira, Cristina |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Cornell University FIOCRUZ UMR5558 |
dc.contributor.author.fl_str_mv |
Castro, Marcelo R. J. [UNESP] Goubert, Clément Carareto, Claudia M. A. [UNESP] Monteiro, Fernando A. Vieira, Cristina |
dc.subject.por.fl_str_mv |
Burst of transposition DnaPipeTE Mariner family Repeatome Rhodnius marabaensis Rhodnius montenegrensis Rhodnius prolixus |
topic |
Burst of transposition DnaPipeTE Mariner family Repeatome Rhodnius marabaensis Rhodnius montenegrensis Rhodnius prolixus |
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. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-12-12T01:56:25Z 2020-12-12T01:56:25Z 2020-02-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3390/genes11020170 Genes, v. 11, n. 2, 2020. 2073-4425 http://hdl.handle.net/11449/200057 10.3390/genes11020170 2-s2.0-85079236359 3425772998319216 0000-0002-0298-1354 |
url |
http://dx.doi.org/10.3390/genes11020170 http://hdl.handle.net/11449/200057 |
identifier_str_mv |
Genes, v. 11, n. 2, 2020. 2073-4425 10.3390/genes11020170 2-s2.0-85079236359 3425772998319216 0000-0002-0298-1354 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genes |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129017726894080 |