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Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its di...

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Autores principales: Gordon, Sean P., Contreras-Moreira, Bruno, Levy, Joshua J., Djamei, Armin, Czedik-Eysenberg, Angelika, Tartaglio, Virginia S., Session, Adam, Martin, Joel, Cartwright, Amy, Katz, Andrew, Singan, Vasanth R., Goltsman, Eugene, Barry, Kerrie, Dinh-Thi, Vinh Ha, Chalhoub, Boulos, Diaz-Perez, Antonio, Sancho, Ruben, Lusinska, Joanna, Wolny, Elzbieta, Nibau, Candida, Doonan, John H., Mur, Luis A. J., Plott, Chris, Jenkins, Jerry, Hazen, Samuel P., Lee, Scott J., Shu, Shengqiang, Goodstein, David, Rokhsar, Daniel, Schmutz, Jeremy, Hasterok, Robert, Catalan, Pilar, Vogel, John P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391716/
https://www.ncbi.nlm.nih.gov/pubmed/32728126
http://dx.doi.org/10.1038/s41467-020-17302-5
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author Gordon, Sean P.
Contreras-Moreira, Bruno
Levy, Joshua J.
Djamei, Armin
Czedik-Eysenberg, Angelika
Tartaglio, Virginia S.
Session, Adam
Martin, Joel
Cartwright, Amy
Katz, Andrew
Singan, Vasanth R.
Goltsman, Eugene
Barry, Kerrie
Dinh-Thi, Vinh Ha
Chalhoub, Boulos
Diaz-Perez, Antonio
Sancho, Ruben
Lusinska, Joanna
Wolny, Elzbieta
Nibau, Candida
Doonan, John H.
Mur, Luis A. J.
Plott, Chris
Jenkins, Jerry
Hazen, Samuel P.
Lee, Scott J.
Shu, Shengqiang
Goodstein, David
Rokhsar, Daniel
Schmutz, Jeremy
Hasterok, Robert
Catalan, Pilar
Vogel, John P.
author_facet Gordon, Sean P.
Contreras-Moreira, Bruno
Levy, Joshua J.
Djamei, Armin
Czedik-Eysenberg, Angelika
Tartaglio, Virginia S.
Session, Adam
Martin, Joel
Cartwright, Amy
Katz, Andrew
Singan, Vasanth R.
Goltsman, Eugene
Barry, Kerrie
Dinh-Thi, Vinh Ha
Chalhoub, Boulos
Diaz-Perez, Antonio
Sancho, Ruben
Lusinska, Joanna
Wolny, Elzbieta
Nibau, Candida
Doonan, John H.
Mur, Luis A. J.
Plott, Chris
Jenkins, Jerry
Hazen, Samuel P.
Lee, Scott J.
Shu, Shengqiang
Goodstein, David
Rokhsar, Daniel
Schmutz, Jeremy
Hasterok, Robert
Catalan, Pilar
Vogel, John P.
author_sort Gordon, Sean P.
collection PubMed
description Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.
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spelling pubmed-73917162020-08-12 Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors Gordon, Sean P. Contreras-Moreira, Bruno Levy, Joshua J. Djamei, Armin Czedik-Eysenberg, Angelika Tartaglio, Virginia S. Session, Adam Martin, Joel Cartwright, Amy Katz, Andrew Singan, Vasanth R. Goltsman, Eugene Barry, Kerrie Dinh-Thi, Vinh Ha Chalhoub, Boulos Diaz-Perez, Antonio Sancho, Ruben Lusinska, Joanna Wolny, Elzbieta Nibau, Candida Doonan, John H. Mur, Luis A. J. Plott, Chris Jenkins, Jerry Hazen, Samuel P. Lee, Scott J. Shu, Shengqiang Goodstein, David Rokhsar, Daniel Schmutz, Jeremy Hasterok, Robert Catalan, Pilar Vogel, John P. Nat Commun Article Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution. Nature Publishing Group UK 2020-07-29 /pmc/articles/PMC7391716/ /pubmed/32728126 http://dx.doi.org/10.1038/s41467-020-17302-5 Text en © This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2020 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
Gordon, Sean P.
Contreras-Moreira, Bruno
Levy, Joshua J.
Djamei, Armin
Czedik-Eysenberg, Angelika
Tartaglio, Virginia S.
Session, Adam
Martin, Joel
Cartwright, Amy
Katz, Andrew
Singan, Vasanth R.
Goltsman, Eugene
Barry, Kerrie
Dinh-Thi, Vinh Ha
Chalhoub, Boulos
Diaz-Perez, Antonio
Sancho, Ruben
Lusinska, Joanna
Wolny, Elzbieta
Nibau, Candida
Doonan, John H.
Mur, Luis A. J.
Plott, Chris
Jenkins, Jerry
Hazen, Samuel P.
Lee, Scott J.
Shu, Shengqiang
Goodstein, David
Rokhsar, Daniel
Schmutz, Jeremy
Hasterok, Robert
Catalan, Pilar
Vogel, John P.
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
title Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
title_full Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
title_fullStr Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
title_full_unstemmed Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
title_short Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
title_sort gradual polyploid genome evolution revealed by pan-genomic analysis of brachypodium hybridum and its diploid progenitors
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391716/
https://www.ncbi.nlm.nih.gov/pubmed/32728126
http://dx.doi.org/10.1038/s41467-020-17302-5
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