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The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits

Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms of subgenome evolution as well as its dynamics and ultimate consequences remains elusive. Here, we report the telomere-to-telomere (T2T) gap-free reference genome of all...

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Autores principales: Shen, Fei, Xu, Shixiao, Shen, Qi, Bi, Changwei, Lysak, Martin A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10368706/
https://www.ncbi.nlm.nih.gov/pubmed/37491530
http://dx.doi.org/10.1038/s41467-023-39800-y
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author Shen, Fei
Xu, Shixiao
Shen, Qi
Bi, Changwei
Lysak, Martin A.
author_facet Shen, Fei
Xu, Shixiao
Shen, Qi
Bi, Changwei
Lysak, Martin A.
author_sort Shen, Fei
collection PubMed
description Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms of subgenome evolution as well as its dynamics and ultimate consequences remains elusive. Here, we report the telomere-to-telomere (T2T) gap-free reference genome of allotetraploid horseradish (Armoracia rusticana) sequenced using a comprehensive strategy. The (epi)genomic architecture and 3D chromatin structure of the A and B subgenomes differ significantly, suggesting that both the dynamics of the dominant long terminal repeat retrotransposons and DNA methylation have played critical roles in subgenome diversification. Investigation of the genetic basis of biosynthesis of glucosinolates (GSLs) and horseradish peroxidases reveals both the important role of polyploidization and subgenome differentiation in shaping the key traits. Continuous duplication and divergence of essential genes of GSL biosynthesis (e.g., FMO(GS-OX), IGMT, and GH1 gene family) contribute to the broad GSL profile in horseradish. Overall, the T2T assembly of the allotetraploid horseradish genome expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish.
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spelling pubmed-103687062023-07-27 The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits Shen, Fei Xu, Shixiao Shen, Qi Bi, Changwei Lysak, Martin A. Nat Commun Article Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms of subgenome evolution as well as its dynamics and ultimate consequences remains elusive. Here, we report the telomere-to-telomere (T2T) gap-free reference genome of allotetraploid horseradish (Armoracia rusticana) sequenced using a comprehensive strategy. The (epi)genomic architecture and 3D chromatin structure of the A and B subgenomes differ significantly, suggesting that both the dynamics of the dominant long terminal repeat retrotransposons and DNA methylation have played critical roles in subgenome diversification. Investigation of the genetic basis of biosynthesis of glucosinolates (GSLs) and horseradish peroxidases reveals both the important role of polyploidization and subgenome differentiation in shaping the key traits. Continuous duplication and divergence of essential genes of GSL biosynthesis (e.g., FMO(GS-OX), IGMT, and GH1 gene family) contribute to the broad GSL profile in horseradish. Overall, the T2T assembly of the allotetraploid horseradish genome expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish. Nature Publishing Group UK 2023-07-25 /pmc/articles/PMC10368706/ /pubmed/37491530 http://dx.doi.org/10.1038/s41467-023-39800-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Shen, Fei
Xu, Shixiao
Shen, Qi
Bi, Changwei
Lysak, Martin A.
The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
title The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
title_full The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
title_fullStr The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
title_full_unstemmed The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
title_short The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
title_sort allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10368706/
https://www.ncbi.nlm.nih.gov/pubmed/37491530
http://dx.doi.org/10.1038/s41467-023-39800-y
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