Codon usage bias and determining forces in green plant mitochondrial genomes.
Codon usage bias and determining forces in green plant mitochondrial genomes.
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DOI：
10.1111/j.1744-7909.2011.01033.x
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发表时间：
2011-04
影响因子：
11.4
通讯作者：
Bin Wang;Jingjing Yuan;Jing Liu;Liang Jin;Jian-Qun Chen
中科院分区：
文献类型：
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作者：
Bin Wang;Jingjing Yuan;Jing Liu;Liang Jin;Jian-Qun Chen
密码子使用偏倚现象已在多种生物体中观察到。随着生物体的进化，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，我们重点关注绿色植物线粒体基因组，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决定力可能发生的变化。在绿色植物的不同谱系之间观察到两种模式：绿藻门和链藻门。在绿藻门谱系中，它们的密码子使用表现出显着的差异（从强 A、T 偏向到强 G、C 偏向）；而在链藻门谱系中，尤其是在陆地植物中，总体密码子使用非常稳定。此外，根据 Nc-GC3s 图和 Akashi 的缩放 χ(2) 检验，我们发现绿藻内的谱系表现出更有力的偏离中性的证据；而链藻门内的谱系很少这样做。这些差异，加上之前基于叶绿体数据的报告，表明植物在陆地上定居后，它们在细胞器基因组中的密码子使用更不愿意受到选择力的影响。
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.