Whole Mitogenome Sequence Alignment Method and its application
The fungal mitochondria possess independent genomes and their conserved protein-coding genes have been frequently used for constructing phylogenetic trees. However, phylogenetic analysis based on full-length alignments of fungal mitogenomes with varied sizes remains underexplored. Recently, the dramatic increase of newly unannotated mitogenomes has created a need of tools for automated full-length mitogenome alignment. We developed WMAF, a novel Python-based tool for sequence alignment. The main principle of the method was to identify conserved regions (i.e., blocks) among multiple mitogenomes and to concatenate sequences of the aligned blocks for subsequent analysis. It overcame recombination effects and eliminated the detection of identical loci across multiple mitogenomes. We further applied WMAF to investigate evolutionary histories of strains within five genera, including Purpureocillium, Fusarium, Saccharomyces, Trichoderma, and Rhizoctonia. The comparative analysis of mitochondrial and nuclear trees demonstrated that WMAF effectively identified major fungal clades. The method will promote the construction of the tree of life for fungi.