Synonymous codons are decoded at different rates during translation elongation, presumably due to the differences in tRNA availability. The biosynthetic cost of each synonymous codon might also differ from each other. Lower cost and higher translation efficiency are both favorable, but optimization of both features is rare. In the plant kingdom, whether the cost-efficiency trade-off/dilemma exists remains largely unknown. To address this, we collected nine well-annotated angiosperms plus additional 60 plant species. We investigated the selection patterns of the cost-efficiency trade-off. At both codon and gene level, the biosynthetic cost and translation efficiency are positively correlated. Higher efficiency is achieved at the expense of higher cost. Interestingly, the genes undergoing stronger selection constraint tend to optimize their cost-efficiency balance. In Arabidopsis, optimized genes are enriched in the most conserved and highly expressed genes. Our study demonstrates the presence of cost-efficiency trade-offs in plants and shows how variation in cost and efficiency interplay at codon and gene levels. Our findings could provide novel perspectives for genome evolution in angiosperms.

中文翻译：

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mRNA 翻译过程中成本和效率之间的权衡很大程度上是由被子植物的自然选择驱动的

在翻译延伸过程中，同义密码子以不同的速率被解码，大概是由于 tRNA 可用性的差异。每个同义密码子的生物合成成本也可能彼此不同。较低的成本和较高的翻译效率都是有利的，但对这两个特征的优化很少见。在植物界，是否存在成本效益权衡/困境在很大程度上仍然未知。为了解决这个问题，我们收集了九种注释良好的被子植物以及另外 60 种植物。我们调查了成本效益权衡的选择模式。在密码子和基因水平上，生物合成成本和翻译效率呈正相关。更高的效率是以更高的成本为代价的。有趣的是，受到更强选择约束的基因往往会优化其成本效益平衡。在拟南芥中，优化的基因富含最保守和高度表达的基因。我们的研究证明了植物中存在成本效益权衡，并展示了成本和效率的变化如何在密码子和基因水平上相互作用。我们的发现可以为被子植物的基因组进化提供新的视角。