*4.6. Assembly of the RNA-Seq Data*

RNA-Seq data from the samples HE1 and HE2 were used for the annotation of additional ORFs. Reads were trimmed with Trimmomatic version 0.36 [84]. The combined trimmed reads of HE1 and HE2 were mapped with the STAR RNA-Seq aligner to the mitochondrial reference sequence of *F. sylvatica*. This mapping was used for a reference-guided assembly of the RNA-Seq data with the software Trinity version 2.8.5 [85] which resulted in 229 mitochondrial transcript contigs.
