College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China.
Funct Integr Genomics. 2024 Mar 1;24(2):45. doi: 10.1007/s10142-024-01316-z.
Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of chloroplast genomes in 36 species from Graciliaceae show that GC range from 0.284 to 0.335, the average GC3 range from 0.135 to 0.243 and the value of ENC range from 35.098 to 42.327, which indicates these genomes are rich in AT and prefer to use codons ending with AT in these species. Nc plot, PR2 plot, neutrality plot analyses and correlation analysis indicate that these biases may be caused by multiple factors, such as natural selection and mutation pressure, but prolonged natural selection is the main driving force influencing codon usage preference. The cluster analysis and phylogenetic analysis show that the differentiation relationship of them is different and indicate that codons with weak or unbiased preferences may also play an irreplaceable role in these species' evolution. In addition, we identified 26 common high-frequency codons and 8-18 optimal codons all ending in A/U in these 36 species. Our results will not only contribute to carrying out transgenic work in Gracilariaceae species to maximize the protein yield in the future, but also lay a theoretical foundation for further exploring systematic classification of them.
石花菜科是一类海洋大型红藻，是琼脂的主要来源，具有重要的经济和生态价值。36 种石花菜科植物的叶绿体基因组密码子使用模式表明，GC 含量范围为 0.284 至 0.335，GC3 平均值范围为 0.135 至 0.243，ENC 值范围为 35.098 至 42.327，这表明这些基因组富含 AT，并且这些物种中偏爱使用以 AT 结尾的密码子。Nc 图、PR2 图、中性绘图分析和相关性分析表明，这些偏好可能是由多种因素引起的，如自然选择和突变压力，但长期的自然选择是影响密码子使用偏好的主要驱动力。聚类分析和系统发育分析表明，它们的分化关系不同，这表明弱偏好或无偏密码子在这些物种的进化中也可能发挥着不可替代的作用。此外，我们在这 36 个物种中鉴定出了 26 个常见的高频密码子和 8-18 个最优密码子，它们都以 A/U 结尾。我们的研究结果不仅有助于未来在石花菜科物种中开展转基因工作，以最大限度地提高蛋白质产量，而且为进一步探讨它们的系统分类奠定了理论基础。
