PDF(Pubmed)
Abstract：
The codon usage bias (CUB) of genes encoded by different species\' genomes varies greatly. The analysis of codon usage patterns enriches our comprehension of genetic and evolutionary characteristics across diverse species. In this study, we performed a genome-wide analysis of CUB and its influencing factors in six sequenced Eimeria species that cause coccidiosis in poultry: Eimeria acervulina, Eimeria necatrix, Eimeria brunetti, Eimeria tenella, Eimeria praecox, and Eimeria maxima. The GC content of protein-coding genes varies between 52.67% and 58.24% among the six Eimeria species. The distribution trend of GC content at different codon positions follows GC1 > GC3 > GC2. Most high-frequency codons tend to end with C/G, except in E. maxima. Additionally, there is a positive correlation between GC3 content and GC3s/C3s, but a significantly negative correlation with A3s. Analysis of the ENC-Plot, neutrality plot, and PR2-bias plot suggests that selection pressure has a stronger influence than mutational pressure on CUB in the six Eimeria genomes. Finally, we identified from 11 to 15 optimal codons, with GCA, CAG, and AGC being the most commonly used optimal codons across these species. This study offers a thorough exploration of the relationships between CUB and selection pressures within the protein-coding genes of Eimeria species. Genetic evolution in these species appears to be influenced by mutations and selection pressures. Additionally, the findings shed light on unique characteristics and evolutionary traits specific to the six Eimeria species.
摘要：
不同物种基因组编码的基因的密码子使用偏好(CUB)差异很大。对密码子使用模式的分析丰富了我们对不同物种的遗传和进化特征的理解。在这项研究中,我们对导致家禽球虫病的六种测序艾美球虫物种的CUB及其影响因素进行了全基因组分析：艾美球虫,艾美球虫Brunetti,艾美耳球虫,艾美球虫praecox,和最大的艾美球虫。在六个艾美球虫物种中，蛋白质编码基因的GC含量在52.67％至58.24％之间变化。GC含量在不同密码子位置的分布趋势遵循GC1>GC3>GC2。大多数高频密码子倾向于以C/G结尾，除了E.maxima。此外,GC3含量与GC3s/C3s呈正相关，但与A3s呈显著负相关。对ENC图的分析，中立情节,和PR2偏倚图表明，在六个艾美耳球虫基因组中，选择压力比突变压力对CUB的影响更大。最后,我们确定了11到15个最佳密码子，GCA,CAG,AGC是这些物种中最常用的最佳密码子。这项研究提供了对CUB与艾美球虫物种蛋白质编码基因内选择压力之间关系的彻底探索。这些物种的遗传进化似乎受到突变和选择压力的影响。此外,这些发现揭示了六种艾美球虫物种特有的独特特征和进化特征。
