College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China.
BMC Genomics. 2023 Sep 11;24(1):538. doi: 10.1186/s12864-023-09586-w.
Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.
红藻是已知的与绿色植物最接近的近亲之一。研究它们基因组的密码子可以帮助我们了解绿色植物祖先的密码子使用模式和特征。通过研究所有可用的红藻的密码子使用模式，发现尽管物种之间存在一些差异，但大多数红藻的高偏向性基因偏好以 GC 结尾的密码子。相关性分析、Nc-GC3s 图、奇偶校验规则 2 图、中性绘图分析、差异蛋白区分析以及内含子和侧翼序列核苷酸含量的比较表明，这种偏向现象可能受到局部突变压力和自然选择的影响，后者在翻译准确性和效率方面是主要因素。值得注意的是，即使在个别物种的低偏向性基因中也可以检测到对翻译准确性的选择。此外，我们首次在除 G. sulphuraria 之外的 7 种红藻中鉴定出 15 个常见的最优密码子，其中大多数与拷贝数最高的 tRNA 基因互补并结合。有趣的是，所有多细胞红藻和个别单细胞红藻的高度退化氨基酸都发现了 tRNA 修饰，这表明高度偏向性基因在翻译中倾向于使用修饰的 tRNA。我们的研究不仅为探索红藻作为绿色植物祖先的密码子使用特征奠定了基础，而且还将有助于未来某些经济红藻的转基因设计和性能。
