State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China.
J Integr Plant Biol. 2011 Apr;53(4):324-34. doi: 10.1111/j.1744-7909.2011.01033.x. Epub 2011 Mar 21.
The phenomenon of codon usage bias has been observed in a wide range of organisms. As organisms evolve, how their codon usage pattern change is still an intriguing question. In this article, we focused on the green plant mitochondrial genomes to analyze the codon usage patterns in different lineages, and more importantly, to investigate the possible change of determining forces during the plant evolution. Two patterns were observed between the separate lineages of green plants: Chlorophyta and Streptophyta. In Chlorophyta lineages, their codon usages showed substantial variation (from strongly A, T-biased to strongly G, C-biased); while in Streptophyta lineages, especially in the land plants, the overall codon usages are interestingly stable. Further, based on the Nc-GC3s plots and Akashi's scaled χ(2) -tests, we found that lineages within Chlorophyta exhibit much stronger evidence of deviating from neutrality; while lineages within Streptophyta rarely do so. Such differences, together with previous reports based on the chloroplast data, suggests that after plants colonized the land, their codon usages in organellar genomes are more reluctant to be shaped by selection force.
密码子使用偏性现象在广泛的生物中都有观察到。随着生物的进化，它们的密码子使用模式如何变化仍然是一个有趣的问题。在本文中，我们专注于绿色植物的线粒体基因组，分析不同谱系中的密码子使用模式，更重要的是，研究植物进化过程中可能改变的决定因素。在绿色植物的不同谱系中观察到两种模式：绿藻门和绿藻门。在绿藻门的谱系中，它们的密码子使用显示出很大的变化（从强烈的 A、T 偏倚到强烈的 G、C 偏倚）；而在绿藻门的谱系中，特别是在陆地植物中，整体密码子使用非常稳定。此外，基于 Nc-GC3s 图和 Akashi 的缩放 χ(2) -检验，我们发现绿藻门内的谱系表现出更强的偏离中性的证据；而绿藻门内的谱系很少如此。这些差异，加上基于叶绿体数据的先前报告，表明植物在登陆后，其细胞器基因组中的密码子使用更不容易受到选择压力的影响。
