A reference genome of the European beech (Fagus sylvatica L.)

  • Background: 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. Findings: Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences 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 Benchmarking with Universal Single-Copy Orthologs (BUSCO) 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. Conclusions: The assembled genome will be 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.
Author:Bagdevi Mishra, Deepak Kumar Gupta, Markus PfenningerORCiDGND, Thomas HicklerORCiD, Ewald Langer, Bora Nam, Juraj Paule, Rahul Sharma, Bartosz Ulaszewski, Joanna Warmbier, Jaroslaw Burczyk, Marco Thines
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/29893845
Parent Title (English):GigaScience
Publisher:Biomed Central
Place of publication:London
Document Type:Article
Year of Completion:2018
Date of first Publication:2018/05/28
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2018/08/16
Tag:forest tree; fungi; genomics; hardwood; hybrid assembly; transcriptomics
Issue:6, giy063
Page Number:9
First Page:1
Last Page:8
© The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Institutes:Geowissenschaften / Geographie / Geographie
Angeschlossene und kooperierende Institutionen / Senckenbergische Naturforschende Gesellschaft
Biowissenschaften / Institut für Ökologie, Evolution und Diversität
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 58 Pflanzen (Botanik) / 580 Pflanzen (Botanik)
Sammlung Biologie / Sondersammelgebiets-Volltexte
Licence (German):License LogoCreative Commons - Namensnennung 4.0