Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Plant cells arose through the endosymbiotic engulfment of a cyanobacterium that subsequently formed the chloroplast genome, enabling plants to develop new critical functions. Almost all chloroplast proteins are now encoded in the nucleus, but some chloroplast protein complexes are jointly encoded by both nuclear and chloroplast genes, which interact to facilitate essential plant functions, such as the photosystems. Allopolyploidy, resulting from the hybridization and genome doubling of two divergent species, can disrupt these fine-tuned cytonuclear interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparental organelle inheritance. Such unequal genome inheritance may affect the conformation of the five cytonuclear complexes in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy and dichotomic divergence in parental species, as well as the effects of recent allopolyploidy in Brassica napus, on genes implicated in cytonuclear complexes. Because the B. napus parental diploid species are paleohexaploids, we first identified paleologous copies of cytonuclear complex genes. We found that these genes are preferentially retained in duplicates, are nearly all transcribed and are undergoing strong purifying selection, in accordance with the ‘gene balance hypothesis’. Subsequently, we compared expression patterns of cytonuclear complex homoeolog genes between resynthesized B. napus individuals and their respective diploid parents. The neo-polyploids showed neither biased sub-genome expression nor homogenization of homoeologs, due to highly conserved parental chloroplast genomes. These findings provide new insights and an innovative framework to understand the impact of cytonuclear interactions on interspecific hybridization and allopolyploid speciation.