Roux Julien, Liu Jialin, Robinson-Rechavi Marc
Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Mol Biol Evol. 2017 Nov 1;34(11):2773-2791. doi: 10.1093/molbev/msx199.
The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.
在脊椎动物祖先中发生了两轮连续的全基因组重复，以及硬骨鱼特有的第三次全基因组重复。大多数重复基因的偏向性丢失使基因组中特定基因（如进化缓慢的基因）得到富集，但这种选择性保留过程尚不清楚。为了了解是什么驱动了重复基因的长期保存，我们根据重复基因的表达模式对其进行了表征。我们使用了一种新的表达富集分析方法TopAnat，将其应用于来自斑马鱼和小鼠数千个基因的原位杂交数据。我们发现，在全基因组重复后，神经系统中的表达是重复基因保留率较高的一个良好预测指标。进一步的分析表明，针对错误折叠或相互作用错误的蛋白质的毒性作用进行的纯化选择，在不可再生的神经组织中尤为强烈，这可能会限制神经系统基因编码序列的进化，从而间接导致全基因组重复后重复基因的保存。因此，全基因组重复极大地促进了脊椎动物辐射演化基础上神经系统深刻新特征进化可用基因工具包的扩展。
