A chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs

Abstract

Background: 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. Results: 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 Mb 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 of the genome in 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. Conclusions: 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.

Genomic basis for drought resistance in European beech forests threatened by climate change

“…We used an improved version of the recently published reference genome for the European beech ( Mishra et al, 2018 ). Contiguity was improved to chromosome level using Hi-C reads with the help of the allhic software after excluding the probable organelle backbones from the earlier assembly that was generated from the Illumina-corrected PacBio reads using Canu assembler ( Mishra et al, 2021 ) accession no. PRJNA450822.…”

Complete Chloroplast Genomes of Fagus sylvatica L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs

“…In beech, due to maternal inheritance of organelles [ 3 ], heteroplasmy can exclusively be caused by mutations. The evidence of multiple integrations of organelle DNA integration with the nuclear genome in beech [ 46 ] and detection of within-individual polymorphisms of cpDNA-related sequences presented in this study suggest that assessing beech diversity with chloroplast related SNPs due to a large occurrence of nuclear encoded of plastid DNA (NUPTs) can lead to uncertain results and should be taken with caution [ 57 ].…”

“…The marker calling was done with Freebayes [ 44 ] with 0.02 minor allele frequency (MAF) and depth of 200x thresholds for variant detection to avoid sequencing error [ 45 ]. To verify the origin of the markers reads were mapped to chromosome 10 of the Fagus sylvatica nuclear assembly [ 46 ].…”

Differences in fine-scale spatial genetic structure of European beech populations along elevational gradients

“…Based on whole-genome sequencing of a subset of 96 samples, ~100k high quality target regions were determined for SPET sequencing by IGATech (IGA Technology Services Srl, Udine, Italy). All 500 F. sylvatica samples were SPET sequenced and sequencing reads were trimmed and mapped to the chromosome level F. sylvatica genome v2(Mishra et al, 2022). Quality trimming was performed using ERNE v1.4.6 (Del Fabbro et al, 2013) with default parameters.…”

“…In order to identify neutral variants for population genetic analysis, the following ltering steps were applied.First, SNPs located in intergenic regions were determined using SnpEff (version 4.3t,Cingolani et al, 2012). For this, an annotation database based on the F. sylvatica reference sequence and gene annotations(Mishra et al, 2022) was built, based on which the effects for each SNP, such as intergenic region variant, missense variant, or intron variant, were inferred. In a second ltering step, SNPs in linkage disequilibrium were ltered out using PLINK (v1.90b6.10),(Purcell et al, 2007) with an ld-window size of 100,000 kb (--ld-window-kb).…”