TY  - JOUR
A1  - Mishra, Bagdevi
A1  - Ulaszewski, Bartosz
A1  - Meger, Joanna
A1  - Aury, Jean-Marc
A1  - Bodénès, Catherine
A1  - Lesur-Kupin, Isabelle
A1  - Pfenninger, Markus
A1  - Da Silva, Corinne
A1  - Gupta, Deepak Kumar
A1  - Guichoux, Erwan
A1  - Heer, Katrin
A1  - Lalanne, Céline
A1  - Labadie, Karine
A1  - Opgenoorth, Lars
A1  - Ploch, Sebastian
A1  - Le Provost, Grégoire
A1  - Salse, Jérôme
A1  - Scotti, Ivan
A1  - Wötzel, Stefan
A1  - Plomion, Christophe
A1  - Burczyk, Jaroslaw
A1  - Thines, Marco
T1  - A chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs
T2  - Frontiers in genetics
N2  - 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.
KW  - chromosomes
KW  - Fagaceae
KW  - genome architecture
KW  - genomics
KW  - Hi-C
KW  - repeat elements
KW  - SNPs
Y1  - 2022
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/73419
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-734198
SN  - 1664-8021
N1  - his study was supported by Grants of the German Science Foundation (Th1632/18-1), National Science Centre, Poland (2012/04/A/NZ9/00F500; 2018/31/F/NZ2/01747), the Polish Ministry of Science, and Higher Education under the program “Regional Initiative of Excellence” in 2019–2022 (Grant No. 008/RID/2018/19), and the LOEWE initiative of the government of Hessen in the framework of the LOEWE Centre for Translational Biodiversity Genomics (TBG). IL received funding from the European Union's Horizon 2020 research and innovation program (GENTREE project, No. 676876). Further funding was received for the validation of the chromosome-scale assembly, sequencing, computing, and services, respectively: INRAE (Ecodiv division) and the Genoscope: the Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 2) France Génomique (ANR-10-INBS-09-08, Beech genome project), Genotoul Bioinformatics Platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12 [Titel anhand dieser DOI in Citavi-Projekt übernehmen] ), 4) the Genome Transcriptome Facility of Bordeaux (grant from Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest ANR-10-EQPX-16-01).
VL  - 12
IS  - art. 691058
SP  - 1
EP  - 18
PB  - Frontiers Media
CY  - Lausanne
ER  -