Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, Hubei, China.
Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, College of Life Science, Jianghan University, Wuhan, Hubei, China.
BMC Genomics. 2024 Oct 8;25(1):945. doi: 10.1186/s12864-024-10825-x.
The Halimedineae are marine green macroalgae that play crucial roles as primary producers in various habitats, including coral reefs, rocky shores, embayments, lagoons, and seagrass beds. Several tropical species have calcified thalli, which contribute significantly to the formation of coral reefs. In this study, we investigated the codon usage patterns and the main factors influencing codon usage bias in 16 chloroplast genomes of the suborder Halimedineae. Nucleotide composition analysis revealed that the codons of these species were enriched in A/U bases and preferred to end in A/U bases, and the distribution of GC content followed a trend of GC1 > GC2 > GC3. 30 optimal codons encoding 17 amino acids were identified, and most of the optimal codons and all of the over-expressed codons preferentially ended with A/U. The neutrality plot, effective number of codons (ENc) plot, and parity rule 2 (PR2) plot analysis indicated that natural selection played a major role in shaping codon usage bias of the most Halimedineae species. The genetic relationships based on their RSCU values and chloroplast protein-coding genes showed the closely related species have similar codon usage patterns. This study describes, for the first time, the codon usage patterns and characterization of Halimedineae chloroplast genomes, and provides new insights into the evolution of this suborder.
卤蕨亚目是海洋绿藻，在各种生境中起着初级生产者的关键作用，包括珊瑚礁、岩石海岸、港湾、泻湖和海草床。一些热带物种具有钙化的藻体，这对珊瑚礁的形成有重要贡献。在这项研究中，我们调查了卤蕨亚目 16 个叶绿体基因组的密码子使用模式和影响密码子使用偏性的主要因素。核苷酸组成分析表明，这些物种的密码子富含 A/U 碱基，并且偏好以 A/U 碱基结尾，GC 含量的分布遵循 GC1 > GC2 > GC3 的趋势。鉴定出 30 个编码 17 种氨基酸的最优密码子，大多数最优密码子和所有过表达密码子都优先以 A/U 结尾。中性绘图、有效密码子数 (ENc) 绘图和奇偶规则 2 (PR2) 绘图分析表明，自然选择在塑造卤蕨亚目大多数物种的密码子使用偏性方面起着主要作用。基于相对同义密码子使用 (RSCU) 值和叶绿体蛋白编码基因的遗传关系表明，亲缘关系密切的物种具有相似的密码子使用模式。本研究首次描述了卤蕨亚目叶绿体基因组的密码子使用模式和特征，并为该亚目的进化提供了新的见解。
