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Retrotranspositional landscape of Asian rice revealed by 3000 genomes

The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the dete...

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Autores principales: Carpentier, Marie-Christine, Manfroi, Ernandes, Wei, Fu-Jin, Wu, Hshin-Ping, Lasserre, Eric, Llauro, Christel, Debladis, Emilie, Akakpo, Roland, Hsing, Yue-Ie, Panaud, Olivier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318337/
https://www.ncbi.nlm.nih.gov/pubmed/30604755
http://dx.doi.org/10.1038/s41467-018-07974-5
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author Carpentier, Marie-Christine
Manfroi, Ernandes
Wei, Fu-Jin
Wu, Hshin-Ping
Lasserre, Eric
Llauro, Christel
Debladis, Emilie
Akakpo, Roland
Hsing, Yue-Ie
Panaud, Olivier
author_facet Carpentier, Marie-Christine
Manfroi, Ernandes
Wei, Fu-Jin
Wu, Hshin-Ping
Lasserre, Eric
Llauro, Christel
Debladis, Emilie
Akakpo, Roland
Hsing, Yue-Ie
Panaud, Olivier
author_sort Carpentier, Marie-Christine
collection PubMed
description The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
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spelling pubmed-63183372019-01-07 Retrotranspositional landscape of Asian rice revealed by 3000 genomes Carpentier, Marie-Christine Manfroi, Ernandes Wei, Fu-Jin Wu, Hshin-Ping Lasserre, Eric Llauro, Christel Debladis, Emilie Akakpo, Roland Hsing, Yue-Ie Panaud, Olivier Nat Commun Article The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events. Nature Publishing Group UK 2019-01-03 /pmc/articles/PMC6318337/ /pubmed/30604755 http://dx.doi.org/10.1038/s41467-018-07974-5 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Carpentier, Marie-Christine
Manfroi, Ernandes
Wei, Fu-Jin
Wu, Hshin-Ping
Lasserre, Eric
Llauro, Christel
Debladis, Emilie
Akakpo, Roland
Hsing, Yue-Ie
Panaud, Olivier
Retrotranspositional landscape of Asian rice revealed by 3000 genomes
title Retrotranspositional landscape of Asian rice revealed by 3000 genomes
title_full Retrotranspositional landscape of Asian rice revealed by 3000 genomes
title_fullStr Retrotranspositional landscape of Asian rice revealed by 3000 genomes
title_full_unstemmed Retrotranspositional landscape of Asian rice revealed by 3000 genomes
title_short Retrotranspositional landscape of Asian rice revealed by 3000 genomes
title_sort retrotranspositional landscape of asian rice revealed by 3000 genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318337/
https://www.ncbi.nlm.nih.gov/pubmed/30604755
http://dx.doi.org/10.1038/s41467-018-07974-5
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