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.