Data from: Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly

A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.本研究对古菌域（Archaea）下代表不同分类类群与生理类群的71个物种开展了全面的计算机模拟分析（in silico）。这些古菌在生理属性——尤其是氧耐受性与能量代谢方面——存在显著差异。我们探究了这些物种的基因与基因组中密码子使用模式的多样性与相似性，重点聚焦于其核心细胞通路，旨在明确这些物种的核心通路在设计层面是否存在潜在共性。通过对密码子使用模式的分析、密码子使用层级线性模型的构建、表达模式分析以及密码子对偏好性研究，本研究证实：古菌核心细胞通路中存在同义密码子偏好性使用的趋势；有效密码子数图（Nc-plot）能够反映不同物种间的生理差异。分析结果显示，需氧古菌在调控基因表达水平方面拥有比仅由密码子使用偏好性所能解释的更大自由度，这一特征可能源于其适应富氧环境后增强的代谢活性。从分类学角度亲缘关系较近的古菌物种，其开放阅读框（ORF）结构模式呈现出显著相似性。在厌氧古菌中，密码子偏好性是决定基因表达的主要因素。本研究还发现，全基因组与核心细胞通路相关基因的密码子对使用模式存在显著差异，且这种差异不仅具有物种特异性，还具备通路特异性，这提示古菌的开放阅读框结构在翻译过程中具备更优的解码准确性。最后，本研究观察到密码子-通路互作会塑造通路的密码子设计模式，其中转录通路展现出显著区别于其他通路的编码频率特征。