Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
Genetics. 2023 Aug 31;225(1). doi: 10.1093/genetics/iyad114.
The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the gene balance hypothesis makes predictions about the expression response to homoeologous exchanges, they have not been empirically tested. We used genomic and transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations to identify homoeologous exchanges, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to homoeologous exchanges than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the B. napus A subgenome. Finally, the expression response to homoeologous exchanges was more variable than the response to whole-genome duplication, suggesting homoeologous exchanges create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time, from homoeolog expression bias to duplicate gene retention.
基因平衡假说提出，选择作用于网络、途径和蛋白质复合物中剂量敏感部分的基因的剂量（即拷贝数），以维持相互作用蛋白质的平衡化学计量，因为化学计量平衡的干扰会导致适应性降低。这种选择被称为剂量平衡选择。剂量平衡选择还假设会限制对剂量变化的表达响应，使剂量敏感基因（编码相互作用蛋白质成员的基因）经历更相似的表达变化。在异源多倍体中，全基因组复制涉及分化谱系的杂交，生物体经常经历同源重组，复制和删除基因组同源区，并改变同源基因对的表达。尽管基因平衡假说对同源交换的表达响应做出了预测，但尚未经过实证检验。我们使用了 10 代来自 6 个合成的、同基因 Brassica napus 系的基因组和转录组数据来鉴定同源交换，分析了表达响应，并测试了基因组失衡的模式。剂量敏感基因组的表达响应变化比剂量不敏感基因组的表达响应变化更小，这表明它们的相对剂量受到限制。对于偏向 B. napus A 亚基因组表达的同源对，这种差异不存在。最后，同源交换的表达响应比全基因组复制的表达响应更具可变性，表明同源交换会导致基因组失衡。这些发现扩展了我们对剂量平衡选择对基因组进化的影响的认识，并可能随着时间的推移将多倍体基因组中的模式联系起来，从同源表达偏向到复制基因保留。
