Cargando…
Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons
Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att) sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029996/ https://www.ncbi.nlm.nih.gov/pubmed/24849372 http://dx.doi.org/10.1371/journal.pone.0097099 |
_version_ | 1782317311802212352 |
---|---|
author | Cruz, Guilherme M. Q. Metcalfe, Cushla J. de Setta, Nathalia Cruz, Edgar A. O. Vieira, Andréia Prata Medina, Rosario Van Sluys, Marie-Anne |
author_facet | Cruz, Guilherme M. Q. Metcalfe, Cushla J. de Setta, Nathalia Cruz, Edgar A. O. Vieira, Andréia Prata Medina, Rosario Van Sluys, Marie-Anne |
author_sort | Cruz, Guilherme M. Q. |
collection | PubMed |
description | Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att) sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification. |
format | Online Article Text |
id | pubmed-4029996 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-40299962014-05-28 Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons Cruz, Guilherme M. Q. Metcalfe, Cushla J. de Setta, Nathalia Cruz, Edgar A. O. Vieira, Andréia Prata Medina, Rosario Van Sluys, Marie-Anne PLoS One Research Article Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att) sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification. Public Library of Science 2014-05-21 /pmc/articles/PMC4029996/ /pubmed/24849372 http://dx.doi.org/10.1371/journal.pone.0097099 Text en © 2014 Cruz et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Cruz, Guilherme M. Q. Metcalfe, Cushla J. de Setta, Nathalia Cruz, Edgar A. O. Vieira, Andréia Prata Medina, Rosario Van Sluys, Marie-Anne Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons |
title | Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons |
title_full | Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons |
title_fullStr | Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons |
title_full_unstemmed | Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons |
title_short | Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons |
title_sort | virus-like attachment sites and plastic cpg islands: landmarks of diversity in plant del retrotransposons |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029996/ https://www.ncbi.nlm.nih.gov/pubmed/24849372 http://dx.doi.org/10.1371/journal.pone.0097099 |
work_keys_str_mv | AT cruzguilhermemq viruslikeattachmentsitesandplasticcpgislandslandmarksofdiversityinplantdelretrotransposons AT metcalfecushlaj viruslikeattachmentsitesandplasticcpgislandslandmarksofdiversityinplantdelretrotransposons AT desettanathalia viruslikeattachmentsitesandplasticcpgislandslandmarksofdiversityinplantdelretrotransposons AT cruzedgarao viruslikeattachmentsitesandplasticcpgislandslandmarksofdiversityinplantdelretrotransposons AT vieiraandreiaprata viruslikeattachmentsitesandplasticcpgislandslandmarksofdiversityinplantdelretrotransposons AT medinarosario viruslikeattachmentsitesandplasticcpgislandslandmarksofdiversityinplantdelretrotransposons AT vansluysmarieanne viruslikeattachmentsitesandplasticcpgislandslandmarksofdiversityinplantdelretrotransposons |