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首页> 外文期刊>BMC Evolutionary Biology >Unlocking a signal of introgression from codons in Lachancea kluyveri using a mutation-selection model
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Unlocking a signal of introgression from codons in Lachancea kluyveri using a mutation-selection model

机译：利用突变选择模型解锁来自Lachancea Kluyveri中的密码子的信号信号

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For decades, codon usage has been used as a measure of adaptation for translational efficiency and translation accuracy of a gene’s coding sequence. These patterns of codon usage reflect both the selective and mutational environment in which the coding sequences evolved. Over this same period, gene transfer between lineages has become widely recognized as an important biological phenomenon. Nevertheless, most studies of codon usage implicitly assume that all genes within a genome evolved under the same selective and mutational environment, an assumption violated when introgression occurs. In order to better understand the effects of introgression on codon usage patterns and vice versa, we examine the patterns of codon usage in Lachancea kluyveri, a yeast which has experienced a large introgression. We quantify the effects of mutation bias and selection for translation efficiency on the codon usage pattern of the endogenous and introgressed exogenous genes using a Bayesian mixture model, ROC SEMPPR, which is built on mechanistic assumptions about protein synthesis and grounded in population genetics. We find substantial differences in codon usage between the endogenous and exogenous genes, and show that these differences can be largely attributed to differences in mutation bias favoring A/T ending codons in the endogenous genes while favoring C/G ending codons in the exogenous genes. Recognizing the two different signatures of mutation bias and selection improves our ability to predict protein synthesis rate by 42% and allowed us to accurately assess the decaying signal of endogenous codon mutation and preferences. In addition, using our estimates of mutation bias and selection, we identify Eremothecium gossypii as the closest relative to the exogenous genes, providing an alternative hypothesis about the origin of the exogenous genes, estimate that the introgression occurred ～6×108 generation ago, and estimate its historic and current selection against mismatched codon usage. Our work illustrates how mechanistic, population genetic models like ROC SEMPPR can separate the effects of mutation and selection on codon usage and provide quantitative estimates from sequence data.
机译：几十年来，密码子使用被用作基因编码序列的翻译效率和翻译准确性的适应的衡量标准。这些密码子使用模式反映了编码序列演变的选择性和突变环境。在同一时期，谱系之间的基因转移已被广泛认为是重要的生物现象。然而，对密码子使用的大多数研究隐含地假设基因组内的所有基因在相同的选择性和突变环境下演变，当发生迟发时侵犯了侵犯的假设。为了更好地了解迟发对密码子使用模式的影响，反之亦然，我们研究了kluyveri，酵母患者的密码子使用模式，这是一种经历大型血气的酵母。我们使用贝叶斯混合模型，ROC SEMPPR来量化突变偏差对内源性和血气外源性基因的密码子使用模式的影响，这是基于关于蛋白质合成的机械假设和群体遗传学。我们在内源性和外源基因之间发现了密码子使用的显着差异，并且表明这些差异可能主要归因于突变偏差的差异，其偏离内源基因中的A / T结束密码子，同时有利于外源基因中的C / G结束密码子。认识到突变偏差和选择的两个不同签名改善了我们预测蛋白质合成率的能力42％，使我们能够准确地评估内源密码子突变和偏好的衰减信号。此外，使用我们对突变偏见和选择的估计，我们将eMetheCium gossypii鉴定为相对于外源基因最接近的，为外源基因的起源提供替代假设，估计速增入发生〜6×108代以前，和估计其历史和目前的选择免受不匹配的密码子使用。我们的工作说明了ROC SEMPPR等机械遗传模型如何分离突变和选择对密码子使用的影响，并提供序列数据的定量估计。

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