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Drosophila parasitoid wasps bears a distinct DNA transposon profile
BACKGROUND: The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genom...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035795/ https://www.ncbi.nlm.nih.gov/pubmed/30002736 http://dx.doi.org/10.1186/s13100-018-0127-2 |
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author | da Silva, Alexandre Freitas Dezordi, Filipe Zimmer Loreto, Elgion Lucio Silva Wallau, Gabriel Luz |
author_facet | da Silva, Alexandre Freitas Dezordi, Filipe Zimmer Loreto, Elgion Lucio Silva Wallau, Gabriel Luz |
author_sort | da Silva, Alexandre Freitas |
collection | PubMed |
description | BACKGROUND: The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species. RESULTS: The different methodologies employed for TE characterization recovered TEs with different features as TE consensus number and size. Moreover, some TEs were detected only by one or few methodologies. RepeatExplorer and dnaPipeTE estimated a low TE content of 5.86 and 4.57% for Braconidae wasp and 5.22% and 7.42% for L. boulardi species, respectively. Both mobilomes are composed by a miscellaneous of ancient and recent elements. Braconidae wasps presented a large diversity of Maverick/Polintons Class II TEs while other TE superfamilies were more equally diverse in both species. Phylogenetic analysis of reconstructed elements showed that vertical transfer is the main mode of transmission. CONCLUSION: Different methodologies should be used complementarity in order to achieve better mobilome characterization. Both wasps genomes have one of the lower mobilome estimates among all Hymenoptera genomes studied so far and presented a higher proportion of Class II than Class I TEs. The large majority of superfamilies analyzed phylogenetically showed that the elements are being inherited by vertical transfer. Overall, we achieved a deep characterization of the mobilome in two non-model parasitoid wasps improving our understanding of their evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-018-0127-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6035795 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60357952018-07-12 Drosophila parasitoid wasps bears a distinct DNA transposon profile da Silva, Alexandre Freitas Dezordi, Filipe Zimmer Loreto, Elgion Lucio Silva Wallau, Gabriel Luz Mob DNA Research BACKGROUND: The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species. RESULTS: The different methodologies employed for TE characterization recovered TEs with different features as TE consensus number and size. Moreover, some TEs were detected only by one or few methodologies. RepeatExplorer and dnaPipeTE estimated a low TE content of 5.86 and 4.57% for Braconidae wasp and 5.22% and 7.42% for L. boulardi species, respectively. Both mobilomes are composed by a miscellaneous of ancient and recent elements. Braconidae wasps presented a large diversity of Maverick/Polintons Class II TEs while other TE superfamilies were more equally diverse in both species. Phylogenetic analysis of reconstructed elements showed that vertical transfer is the main mode of transmission. CONCLUSION: Different methodologies should be used complementarity in order to achieve better mobilome characterization. Both wasps genomes have one of the lower mobilome estimates among all Hymenoptera genomes studied so far and presented a higher proportion of Class II than Class I TEs. The large majority of superfamilies analyzed phylogenetically showed that the elements are being inherited by vertical transfer. Overall, we achieved a deep characterization of the mobilome in two non-model parasitoid wasps improving our understanding of their evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-018-0127-2) contains supplementary material, which is available to authorized users. BioMed Central 2018-07-07 /pmc/articles/PMC6035795/ /pubmed/30002736 http://dx.doi.org/10.1186/s13100-018-0127-2 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research da Silva, Alexandre Freitas Dezordi, Filipe Zimmer Loreto, Elgion Lucio Silva Wallau, Gabriel Luz Drosophila parasitoid wasps bears a distinct DNA transposon profile |
title | Drosophila parasitoid wasps bears a distinct DNA transposon profile |
title_full | Drosophila parasitoid wasps bears a distinct DNA transposon profile |
title_fullStr | Drosophila parasitoid wasps bears a distinct DNA transposon profile |
title_full_unstemmed | Drosophila parasitoid wasps bears a distinct DNA transposon profile |
title_short | Drosophila parasitoid wasps bears a distinct DNA transposon profile |
title_sort | drosophila parasitoid wasps bears a distinct dna transposon profile |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035795/ https://www.ncbi.nlm.nih.gov/pubmed/30002736 http://dx.doi.org/10.1186/s13100-018-0127-2 |
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