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The Triticum-Aegilops complex provides ideal models for the study of polyploidization, and mitochondrial genomes (mtDNA) can be used to trace cytoplasmic inheritance and energy production following polyploidization. In this study, gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled. Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T. turgidum (genome formula AABB), and that this mtDNA was then passed on to the hexaploid T. aestivum (AABBDD). T urartu (AA) was the paternal parent of T. timopheevii (AAGG), and an earlier Ae. tauschii (DD) was the maternal parent of Ae. cylindrica (CCDD). Genic sequences were highly conserved within species, but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation. Four highly variable mitochondrial genes (atp6, cob, nad6, and nad9) were established as marker genes for Triticum and Aegilops species identification. The BB/GG-specific atp6 and cob genes, which were imported from the nuclear genome, could facilitate identification of their diploid progenitors. Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae. speltoides (SS). These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA, advancing understanding of energy supply and adaptation in wheat species. [ABSTRACT FROM AUTHOR]