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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

hal.structure.identifierSenckenberg biodiversität und klima forschungszentrum [BIK-F]
hal.structure.identifierGoethe University Frankfurt
dc.contributor.authorMISHRA, Bagdevi
hal.structure.identifierKazimierz Wielki University [UKW]
dc.contributor.authorULASZEWSKI, Bartosz
hal.structure.identifierKazimierz Wielki University [UKW]
dc.contributor.authorMEGER, Joanna
hal.structure.identifierLaboratoire de Bioinformatique pour la Génomique et la Biodiversité [LBGB]
dc.contributor.authorAURY, Jean-Marc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBODÉNÈS, Catherine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierHelixVenture
hal.structure.identifierPhilipps Universität Marburg = Philipps University of Marburg
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierSenckenberg biodiversität und klima forschungszentrum [BIK-F]
dc.contributor.authorPFENNINGER, Markus
hal.structure.identifierLaboratoire de Bioinformatique pour la Génomique et la Biodiversité [LBGB]
dc.contributor.authorDA SILVA, Corinne
hal.structure.identifierGoethe University Frankfurt
hal.structure.identifierSenckenberg biodiversität und klima forschungszentrum [BIK-F]
hal.structure.identifierBiodiversity and Climate Research Centre (BiK-F) [LOEWE]
dc.contributor.authorGUPTA, Deepak
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGUICHOUX, Erwan
hal.structure.identifierAlbert-Ludwigs-Universität Freiburg
hal.structure.identifierPhilipps Universität Marburg = Philipps University of Marburg
dc.contributor.authorHEER, Katrin
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLALANNE, Céline
hal.structure.identifierGenoscope - Centre national de séquençage [Evry] [GENOSCOPE]
dc.contributor.authorLABADIE, Karine
hal.structure.identifierPhilipps Universität Marburg = Philipps University of Marburg
dc.contributor.authorOPGENOORTH, Lars
hal.structure.identifierSenckenberg biodiversität und klima forschungszentrum [BIK-F]
dc.contributor.authorPLOCH, Sebastian
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorSALSE, Jérôme
hal.structure.identifierEcologie des Forêts Méditerranéennes [URFM]
dc.contributor.authorSCOTTI, Ivan
hal.structure.identifierSenckenberg biodiversität und klima forschungszentrum [BIK-F]
hal.structure.identifierGoethe University Frankfurt
dc.contributor.authorWÖTZEL, Stefan
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierKazimierz Wielki University [UKW]
dc.contributor.authorBURCZYK, Jaroslaw
hal.structure.identifierSenckenberg biodiversität und klima forschungszentrum [BIK-F]
hal.structure.identifierGoethe University Frankfurt
hal.structure.identifierBiodiversity and Climate Research Centre (BiK-F) [LOEWE]
dc.contributor.authorTHINES, Marco
dc.date.issued2022-02-08
dc.identifier.issn1664-8021
dc.description.abstractEnThe 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.
dc.description.sponsorshipOrganisation et montée en puissance d'une Infrastructure Nationale de Génomique
dc.description.sponsorshipPlateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur "
dc.language.isoen
dc.publisherFrontiers Media
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enchromosomes
dc.subject.enFagaceae
dc.subject.engenome architecture
dc.subject.engenomics
dc.subject.enHi-C
dc.subject.enrepeat elements
dc.subject.enSNPs
dc.title.enA Chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat Content and distribution of SNPs
dc.typeArticle de revue
dc.identifier.doi10.3389/fgene.2021.691058
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences de l'environnement
dc.description.sponsorshipEuropeOptimising the management and sustainable use of forest genetic resources in Europe
bordeaux.journalFrontiers in Genetics
bordeaux.page691058
bordeaux.volume12
bordeaux.peerReviewedoui
hal.identifierhal-03602006
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03602006v1
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