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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...

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Autores principales: Cruz, Guilherme M. Q., Metcalfe, Cushla J., de Setta, Nathalia, Cruz, Edgar A. O., Vieira, Andréia Prata, Medina, Rosario, Van Sluys, Marie-Anne
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
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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.
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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
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