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A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, w...

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Autores principales: Mishra, Bagdevi, Ulaszewski, Bartosz, Meger, Joanna, Aury, Jean-Marc, Bodénès, Catherine, Lesur-Kupin, Isabelle, Pfenninger, Markus, Da Silva, Corinne, Gupta, Deepak K, Guichoux, Erwan, Heer, Katrin, Lalanne, Céline, Labadie, Karine, Opgenoorth, Lars, Ploch, Sebastian, Le Provost, Grégoire, Salse, Jérôme, Scotti, Ivan, Wötzel, Stefan, Plomion, Christophe, Burczyk, Jaroslaw, Thines, Marco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862710/
https://www.ncbi.nlm.nih.gov/pubmed/35211148
http://dx.doi.org/10.3389/fgene.2021.691058
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author Mishra, Bagdevi
Ulaszewski, Bartosz
Meger, Joanna
Aury, Jean-Marc
Bodénès, Catherine
Lesur-Kupin, Isabelle
Pfenninger, Markus
Da Silva, Corinne
Gupta, Deepak K
Guichoux, Erwan
Heer, Katrin
Lalanne, Céline
Labadie, Karine
Opgenoorth, Lars
Ploch, Sebastian
Le Provost, Grégoire
Salse, Jérôme
Scotti, Ivan
Wötzel, Stefan
Plomion, Christophe
Burczyk, Jaroslaw
Thines, Marco
author_facet Mishra, Bagdevi
Ulaszewski, Bartosz
Meger, Joanna
Aury, Jean-Marc
Bodénès, Catherine
Lesur-Kupin, Isabelle
Pfenninger, Markus
Da Silva, Corinne
Gupta, Deepak K
Guichoux, Erwan
Heer, Katrin
Lalanne, Céline
Labadie, Karine
Opgenoorth, Lars
Ploch, Sebastian
Le Provost, Grégoire
Salse, Jérôme
Scotti, Ivan
Wötzel, Stefan
Plomion, Christophe
Burczyk, Jaroslaw
Thines, Marco
author_sort Mishra, Bagdevi
collection PubMed
description The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
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spelling pubmed-88627102022-02-23 A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs Mishra, Bagdevi Ulaszewski, Bartosz Meger, Joanna Aury, Jean-Marc Bodénès, Catherine Lesur-Kupin, Isabelle Pfenninger, Markus Da Silva, Corinne Gupta, Deepak K Guichoux, Erwan Heer, Katrin Lalanne, Céline Labadie, Karine Opgenoorth, Lars Ploch, Sebastian Le Provost, Grégoire Salse, Jérôme Scotti, Ivan Wötzel, Stefan Plomion, Christophe Burczyk, Jaroslaw Thines, Marco Front Genet Genetics The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate. Frontiers Media S.A. 2022-02-08 /pmc/articles/PMC8862710/ /pubmed/35211148 http://dx.doi.org/10.3389/fgene.2021.691058 Text en Copyright © 2022 Mishra, Ulaszewski, Meger, Aury, Bodénès, Lesur-Kupin, Pfenninger, Da Silva, Gupta, Guichoux, Heer, Lalanne, Labadie, Opgenoorth, Ploch, Le Provost, Salse, Scotti, Wötzel, Plomion, Burczyk and Thines. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Mishra, Bagdevi
Ulaszewski, Bartosz
Meger, Joanna
Aury, Jean-Marc
Bodénès, Catherine
Lesur-Kupin, Isabelle
Pfenninger, Markus
Da Silva, Corinne
Gupta, Deepak K
Guichoux, Erwan
Heer, Katrin
Lalanne, Céline
Labadie, Karine
Opgenoorth, Lars
Ploch, Sebastian
Le Provost, Grégoire
Salse, Jérôme
Scotti, Ivan
Wötzel, Stefan
Plomion, Christophe
Burczyk, Jaroslaw
Thines, Marco
A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs
title A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs
title_full A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs
title_fullStr A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs
title_full_unstemmed A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs
title_short A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs
title_sort chromosome-level genome assembly of the european beech (fagus sylvatica) reveals anomalies for organelle dna integration, repeat content and distribution of snps
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862710/
https://www.ncbi.nlm.nih.gov/pubmed/35211148
http://dx.doi.org/10.3389/fgene.2021.691058
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