Complete Mitochondrial Genome of Taxus wallichiana

We used a hybrid BGI and Nanopore strategy to assemble the Taxus wallichiana mitogenome. Plant mitochondrial assemblies were first performed using the default parameters of GetOrganelle software (default parameters: v1.7.5) on second generation DNA sequencing data to obtain a graphical representation of the mitochondrial genome. The T.wallichiana mitogenome was then visualized using Bandage software and single stretches of the chloroplast and nuclear genomes were manually removed . Finally, the Nanopore data was compared to the graphical mitogenome fragments using BWA software and the resulting Nanopore data was used to resolve the repetitive sequence regions of the graphical plant mitogenome. The T.wallichiana mitogenome was finally obtained by the above method. We used Geseq to annotate the T.wallichiana mitogenome genome of ,  and Arabidopsis thaliana was selected as the reference genome for the protein-coding genes (PCGs) of the mitogenome. The tRNA and rRNA of the mitogenome were annotated using tRNAscan-SE and BLASTN, respectively. When errors were made in the annotation of the mitogenome, Apollo was used to manually correct the errors.