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

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.

植物细胞起源于对蓝细菌的内共生吞噬（endosymbiotic engulfment），该蓝细菌后续演化形成叶绿体基因组（chloroplast genome），使植物得以发育出全新的关键功能。如今几乎所有叶绿体蛋白均由核基因组编码，但部分叶绿体蛋白复合物（chloroplast protein complexes）由核基因与叶绿体基因共同编码，二者协同作用以维持植物的核心生命活动，例如光系统（photosystems）。
异源多倍体（allopolyploidy）由两个分化物种的杂交及基因组加倍形成，其会破坏这些精细调控的核质互作（cytonuclear interactions）：新形成的异源多倍体物种面临的是双亲核染色体与单亲细胞器遗传的不均等遗传模式。这种不均等的基因组遗传可能会影响异源多倍体中五种核质复合物（cytonuclear complexes）的构象。
本研究以芸苔属（Brassica）为模式体系，探究了亲本物种的古多倍体（paleopolyploidy）与二叉分化（dichotomic divergence），以及甘蓝型油菜（Brassica napus）近期形成的异源多倍化，对核质复合物相关基因的影响。由于甘蓝型油菜的二倍体亲本均为古六倍体（paleohexaploids），我们首先鉴定了核质复合物基因的古同源拷贝（paleologous copies）。我们发现，这类基因优先以重复形式保留，几乎全部都能转录，且正经历强烈的纯化选择，这与基因平衡假说（gene balance hypothesis）相符。
随后，我们比较了人工合成的甘蓝型油菜个体与其对应二倍体亲本的核质复合物部分同源基因（homoeolog genes）表达模式。由于亲本叶绿体基因组高度保守，这些新形成的多倍体既未表现出亚基因组表达偏好性，也未出现部分同源基因的均质化（homogenization of homoeologs）现象。上述研究结果为理解核质互作对种间杂交及异源多倍体物种形成的影响提供了全新视角与创新性研究框架。