WMAF: One novel method for whole mitogenome alignment in fungi and its application in phylogenetic analysis

Fungal mitogenomes are significant for phylogenetic studies, however, constructing trees from full-length mitogenomes with varied sizes remains challenging. Recently, the dramatic increase of newly unannotated mitogenomes has created an urgent need for automated alignment tools. To address this, we developed WMAF, a novel Python-based tool that aligns full-length fungal mitogenomes by identifying and concatenating conserved genomic blocks. It overcomes recombination effects and prevents redundant locus detection. We further applied WMAF to five diverse genera, including Purpureocillium, Fusarium, Saccharomyces, Trichoderma, and Rhizoctonia, and generated mitochondrial trees that effectively identified intrageneric clades, as validated by nuclear trees. The method provides a foundation for advancing fungal phylogenetics and constructing the fungal tree of life.