The mitochondrial genome sequence of Fagus sylvatica L. as a source for taxonomic marker development in the Fagales

The European beech, Fagus sylvatica L. is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. We assembled and annotated the complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. based on Illumina MiSeq reads and validated it using long reads from nanopore MinION sequencing. The circular genome is 504,715 bp in length and contains 58 genes with predicted function, including 35 protein-coding, 20 tRNA and 3 rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of mitochondrial genetic markers specific for a taxon of interest, the tool SNPtax was developed and applied to preselect genic SNPs potentially specific for different taxa within the Fagales. Further validation of a few SNPs resulted in the development of four CAPS markers specific for Fagales, Fagaceae, or Fagus, respectively, when considering individuals of about 60 species of deciduous trees and conifers included in the marker validation. The marker set is suitable to identify Fagus species in DNA samples from tree tissues or wood products, including composite wood products.