Supporting data for "A reference genome of the European Beech (Fagus sylvatica L.)"

Dataset type: Genomic, Transcriptomic
Data released on May 31, 2018

Mishra B; Gupta DK; Pfenninger M; Hickler T; Langer E; Nam B; Paule J; Sharma R; Ulaszewski B; Warmbier J; Burczyk J; Thines M (2018): Supporting data for "A reference genome of the European Beech (Fagus sylvatica L.)" GigaScience Database.


The European Beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.
Using a hybrid assembly approach with Illumina reads with short- and long-insert libraries, coupled with long PacBio reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12 % of Ns. A BUSCO (Benchmarking with Universal Single-Copy Orthologs) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high molecular weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.
The assembled genome is a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g. involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.

Additional details

Read the peer-reviewed publication(s):

Mishra, B., Gupta, D. K., Pfenninger, M., Hickler, T., Langer, E., Nam, B., … Thines, M. (2018). A reference genome of the European beech (Fagus sylvatica L.). GigaScience, 7(6). doi:10.1093/gigascience/giy063

Additional information:

Accessions (data included in GigaDB):

BioProject: PRJEB24056
ENA: OIVN01000000

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
FR-Bhaga_DNA28930 European beechFagus sylvatica Description:DNA extracted from ~100 leaf buds of a...
Alternative accession-BioProject:PRJEB24056
Analyte type:RNA
FR-Bhaga-RNA28930 European beechFagus sylvatica Description:RNA extracted from dormant leaf tissue...
Alternative accession-BioProject:PRJEB24056
Alternative accession-SRA Experiment:ERX2326491,ER...
Displaying 1-2 of 2 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
Coding SequenceFASTA108.27 MB2018-05-18
annotationUNKNOWN100.47 MB2018-05-18
protein sequenceUNKNOWN36.76 MB2018-05-18
otherTEXT1.9 KB2018-05-18
scriptPython1.08 KB2018-05-18
scriptPython0.52 KB2018-05-18
scriptPython1.54 KB2018-05-18
scriptPython1.24 KB2018-05-18
scriptPython1.22 KB2018-05-18
otherTEXT1.7 KB2018-05-18
Displaying 11-20 of 31 File(s).
Funding body Awardee Award ID Comments
LOEWE M Pfenninger TBG
National Science Center Poland (NCN) B Ulaszewski 2012/04/A/NZ9/00500
LOEWE T Hickler BiK-F
Date Action
May 31, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy063