Two new Polyporales mitochondrial genomes (Amyloporia xantha and Taiwanofungus gaoligongensis) uncover gene rearrangements, intron dynamics, and broad phylogeny across Basidiomycota

Polyporales, a large order of Basidiomycota, comprises a vast diversity of fungal species that fulfill diverse ecological functions and play critical roles in ecosystem functioning. Their mitochondrial genomes provide an important basis for understanding their evolution and adaptation. In this study, we characterize the complete mitochondrial genomes of two Polyporales species, Amyloporia xantha and Taiwanofungus gaoligongensis , and the findings are expected to deepen our understanding of the origin, evolution, and genetic diversity of Polyporales, as well as offer novel insights into their taxonomic classification and ecological adaptation. It should be noted that the name Taiwanofungus gaoligongensis has not yet been validly published under the International Code of Nomenclature for algae, fungi, and plants (ICN). Its use in this manuscript is solely for convenient reference to the studied strain and does not constitute formal nomenclatural validation. This study employed high-throughput sequencing technology to sequence and assemble the mitochondrial genomes of two species from Polyporales, A. xantha and T. gaoligongensis , and compared them with other mitochondrial genomes of Polyporales fungi. The results revealed complete mitochondrial genomes for both A. xantha and T. gaoligongensis , with total sizes ranging from 44,769 to 110,713 bp. Comparative analysis based on gene content, gene length, and tRNA usage indicated significant differences in genetic composition and tRNA utilization between the two mitochondrial genomes. Codon analysis suggested that gene evolution in Polyporales species is the result of a complex interplay of various factors, with a substantial influence from natural selection. Comparative mitochondrial genomic analysis detected large-scale gene rearrangements within the Polyporales mitochondrial genomes, involving gene translocations and positional exchanges. Intron analysis indicated that the size differences between the two mitochondrial genomes are considerable, with introns being the primary factor contributing to mitochondrial genome size variation, while intergenic regions play a secondary role. Furthermore, Polyporales species frequently undergo intron loss/gain events during their evolutionary processes. Phylogenetic analyses based on Bayesian Inference (BI) and Maximum Likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, indicating that A. xantha forms a sister lineage to the Taiwanofungus clade comprising T. gaoligongensis and T. camphoratus . This study characterizes the complete mitochondrial genomes of A. xantha and the T. gaoligongensis strain. It provides preliminary molecular evidence for the taxonomic status of Amyloporia and Taiwanofungus , and improves our understanding of the classification and evolutionary history of Polyporales species.