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In this study, the mitogenome of  Hannaella oryzae  was sequenced by next-generation sequencing (NGS) and successfully assembled. The  H. oryzae  mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of  H. oryzae  partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the  cox1  gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the  H. oryzae cox1  gene may have different origins. Gene arrangement analysis revealed that  H. oryzae  contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein  H. oryzae  was closely related to  Tremella fuciformis . This study represents the first report of mitogenome for the  Hannaella  genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny