Assembly of mitochondrial genomes
Sequencing reads were trimmed and filtered for quality using Trimmomatic v0.36 (Bolger, Lohse, & Usadel, 2014) before use with the GetOrganelle v1.7.3.5 tool (Jin et al., 2020) with the parameters -R 10 -k 21,45,65,85,105 -F fungus_mt for de novo assembly incorporating the SPAdes v3.13.0 assembler (Prjibelski, Antipov, Meleshko, Lapidus, & Korobeynikov, 2020) and Bowtie2 v2.4.2 (Langmead & Salzberg, 2012). Protein-coding sequences were predicted using Mitos2 webserver (Donath et al., 2019) using the RefSeq 89 Fungi database. Coding sequences were manually inspected using Geneious Prime software v2022.2.1 (Biomatters Ltd., New Zealand). Mitochondrial circular map was drawn using OGDRAW v1.3.1 (Greiner, Lehwark, & Bock, 2019). Newly assembled mitochondrial genomes were submitted to the NCBI Genbank under accessions listed in TABLE 1.