Institute of Genomic Medicine/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China.
Mol Phylogenet Evol. 2012 Jan;62(1):206-13. doi: 10.1016/j.ympev.2011.09.013. Epub 2011 Oct 21.
Marine unicellular cyanobacteria, represented by Synechococcus and Prochlorococcus, dominate the total phytoplankton biomass and production in oligotrophic ocean. In this study, we employed comparative genomics approaches to extensively investigate synonymous codon usage bias and evolutionary rates in a large number of closely related species of marine unicellular cyanobacteria. Although these two groups of marine cyanobacteria have a close phylogenetic relationship, we find that they are highly divergent not only in codon usage patterns but also in the driving forces behind the diversification. It is revealed that in Prochlorococcus, mutation and genome compositional constraints are the main forces contributing to codon usage bias, whereas in Synechococcus, translational selection. In addition, nucleotide substitution rate analysis indicates that they are not evolving at a constant rate after the divergence and that the average d(N)/d(S) values of core genes in Synechococcus are significantly higher than those in Prochlorococcus. Our evolutionary genomic analysis provides the first insight into codon usage, evolutionary genetic mechanisms and environmental adaptation of Synechococcus and Prochlorococcus after divergence.
海洋单细胞蓝藻，以聚球藻和聚磷菌为代表，在贫营养海洋中占据着浮游植物生物量和生产力的主导地位。在这项研究中，我们采用比较基因组学方法，对大量亲缘关系密切的海洋单细胞蓝藻的同义密码子使用偏好性和进化速率进行了广泛的研究。虽然这两组海洋蓝藻具有密切的系统发育关系，但我们发现它们不仅在密码子使用模式上存在很大差异，而且在导致多样化的驱动力上也存在很大差异。结果表明，在聚磷菌中，突变和基因组组成的限制是导致密码子使用偏好性的主要因素，而在聚球藻中，则是翻译选择。此外，核苷酸取代率分析表明，在分化后它们并不是以恒定的速率进化的，而且聚球藻核心基因的平均 d（N）/d（S）值明显高于聚磷菌。我们的进化基因组分析首次深入了解了聚球藻和聚磷菌在分化后的密码子使用、进化遗传机制和环境适应。
