*Article* **Mitochondrial Genome of** *Fagus sylvatica* **L. as a Source for Taxonomic Marker Development in the Fagales**

**Malte Mader 1,**†**, Hilke Schroeder 1,**†**, Thomas Schott 1, Katrin Schöning-Stierand 1,2, Ana Paula Leite Montalvão 1, Heike Liesebach 1, Mirko Liesebach 1, Barbara Fussi <sup>3</sup> and Birgit Kersten 1,\***


Received: 30 July 2020; Accepted: 24 September 2020; Published: 27 September 2020

**Abstract:** 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. The complete DNA sequence of the mitochondrial genome of *Fagus sylvatica* L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for *Fagus*, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus *Fagus* in DNA samples from tree tissues or wood products, including wood composite products.

**Keywords:** mitochondrial genome; genome assembly; *Fagus*; Fagaceae; Fagales; molecular marker; mitochondrial marker; taxon assignment; CAPS marker; SNP
