We determined the complete nucleotide sequence of the 41 719 bp mitochondrial genome of the methylotrophic yeast Hansenula polymorpha strain DL-1. It contains genes for three subunits of cytochrome oxidase (cox1, cox2 and cox3), three subunits of ATP synthase (atp6, atp8 and atp9), seven subunits of NADH dehydrogenase (nad1-6 and nad4L), apocytochrome b (cob), four endonuclease/maturase homologs, a ribosomal protein (rps3), large and small rRNAs and a complete set of tRNAs. The structural genes are organized in two major transcriptional units. Phylogenetic, gene content and gene order analyses revealed the close phylogenetic relationship between H. polymorpha and Brettanomyces custersianus, and support the assignment of strain DL-1 to a separate genus rather than including it in the polyphyletic genus Pichia.
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