Simulation of the evolution of codon usage in cpDNA

The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant psbA gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of plan...被子植物（Angiosperm）psbA基因（psbA gene）的密码子使用模式，有悖于开花植物叶绿体基因的典型特征，却与植物界（Plantae）部分类群——尤其是绿植物支系（Chlorobionta）——中高表达质体基因的密码子使用模式极为相似。这类基因的密码子偏好性模式，提示其曾经历针对一组翻译最优密码子的选择作用；但相较于绿藻类群等支系中的高表达质体基因，被子植物psbA基因对这类最优密码子的偏好程度要弱得多。目前已有两种假说用以解释上述观测结果：其一，当前开花植物psbA基因仅受到较弱的翻译效率选择约束；其二，该基因当前不存在任何选择约束，我们所观测到的仅是祖先密码子适应性的残留信号，这类信号正处于突变压力下的退化过程中。我们通过整合了plan...（原文未完整给出）的上下文依赖突变特性的模拟研究，对上述两种模型展开检验。