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Data released on May 31, 2018

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

Mishra, B; Gupta, D, K; 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. http://dx.doi.org/10.5524/100461 RIS BibTeX Text

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 beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.

Contact Submitter

Additional information:

www.beechgenome.net

Accessions (data included in GigaDB):

BioProject: PRJEB24056
ENA: OIVN01000000

Keywords:

forest tree fungi genomics hardwood hybrid assembly transcriptomics 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100461.png

Funding:

  • Funding body - LOEWE
  • Comment - TBG
  • Awardee - M Pfenninger
  • Funding body - National Science Center Poland (NCN)
  • Award ID - 2012/04/A/NZ9/00500
  • Awardee - B Ulaszewski
  • Funding body - LOEWE
  • Comment - IPF
  • Awardee - M Thines
  • Funding body - LOEWE
  • Comment - BiK-F
  • Awardee - T Hickler

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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
...
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FR-Bhaga-RNA28930 European beechFagus sylvatica Description:RNA extracted from dormant leaf tissue...
Alternative accession-BioProject:PRJEB24056
Alternative accession-SRA Experiment:ERX2326491,ER...
...
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Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
otherUNKNOWN0.31 KB2018-05-18
otherUNKNOWN0.31 KB2018-05-18
otherUNKNOWN0.32 KB2018-05-18
otherUNKNOWN0.32 KB2018-05-18
otherUNKNOWN0.33 KB2018-05-18
otherUNKNOWN0.34 KB2018-05-18
scriptPython0.51 KB2018-05-18
scriptPython0.52 KB2018-05-18
scriptPython0.97 KB2018-05-18
scriptPython1.01 KB2018-05-18
Displaying 1-10 of 31 File(s).

History:

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