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Plants rely on finely tuned coordination among nuclear, mitochondrial, and chloroplast genomes to assemble essential multisubunit cytonuclear complexes. Genome merging and duplication can disrupt this co-evolution and the stoichiometric balances. We conducted a multidisciplinary analysis on the quantification and qualification of organelles, copy number of organelle DNAs, and gene expression changes associated with auto- and allopolyploidization in
Arabidopsis thaliana and
A. lyrata. Our results show that changes in organelle number, organelle genome copy number, and gene expression after whole-genome duplication and/or genome merging is organelle specific and vary across generations. These insights advance our understanding on the stoichiometric compensation mechanisms and polyploid genome evolution.
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