Abstract
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.
Highlights
Many lowland and mountainous forests in Central Europe are dominated by the European Beech (Fagus sylvatica) (Durrant et al, 2016)
3.1.1 Genomic Composition and Completeness The final assembly of the Bhaga genome was based on hybrid assembly of PacBio and Illumina reads as well as scaffolding using a Hi-C library
It was resolved into 12 chromosomes, spanning 535.4 Mb of the genome and 155 unassigned contigs of 4.9 Mb that to 79% consisted of unplaced repeat regions that precluded their unequivocal placement
Summary
Many lowland and mountainous forests in Central Europe are dominated by the European Beech (Fagus sylvatica) (Durrant et al, 2016). For the selection of drought-resistant genotypes, whole genome sequences of trees that thrive in comparatively dry conditions and the comparison with trees that are declining in drier conditions are necessary to identify genes associated with tolerating these adverse conditions (Pfenninger et al, 2020). Such genome-wide association studies rely on well-assembled reference genomes onto which genome data from large-scale resequencing projects can be mapped [e.g., (Atwell et al, 2010)]
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