Abstract: Magnoliaceae is primitive angiosperm with important economic, medicinal and ornamental values. Codon is the core element of translation in central dogma, and its characterics analysis of coding region is important to study the gene function and phylogeneitc evolution. At present, 29 chloroplast genomes of Magnoliaceae have been successfully assembled and annotated. Therefore, this paper collected the chloroplast genomes of Magnoliaceae and systematically analyzed the codon usage profiling of chloroplast genomesand decoded the phylogenetic relationship among the 29 Magnoliaceae plants. The results illustrated that synonymous codons and optimal codons in 29 chloroplast genomes from Magnoliaceae had the same codon usage preference and ending with A/U. The natural selection was the main factor in codon preference. Furthermore, the phylogenetic trees from 29 Magnoliaceae chloroplasts was constructed by using whole genome sequences, CDS sequences and codon preference RSCU values, respectively. It was found that the phylogenetic relationship from codon usage preference was significantly different with others, while the phylogenetic trees from chloroplast whole genomes and CDS sequences were closer to the true relationship among 29 Magnoliaceae plants. Those results further supported that the base mutation and non-coding sequences played an important role in the evolution process of organisms.

Key words: Magnoliaceae, chloroplast genome, codon usage, phylogenetic tree

摘要： 木兰科植物是具有重要经济、药用和观赏等价值的原始被子植物，密码子是基因编码区蛋白翻译的核心元件，分析基因组编码区密码子的使用特征，对基因功能和系统进化研究具有重要意义。目前木兰科植物已有29个物种的叶绿体基因组被成功解析和注释。收集已有的木兰科植物叶绿体基因组，系统解析叶绿体基因组编码区的密码子使用特征，并阐释了木兰科植物间的亲缘进化关系。结果表明，29种木兰科植物的叶绿体基因组编码区的同义密码子和最优密码子使用偏好相同，均以A/U结尾，自然选择是叶绿体编码区密码子偏好形成的主要原因。此外，基于29种木兰科植物叶绿体基因组、CDS序列以及密码子偏好特征RSCU值分别构建了系统进化树，分析发现,基于密码子偏好特征的物种间进化关系明显不同于前两者，而叶绿体基因组和CDS序列构建的进化关系更接近物种的真实分类，该结果也进一步支持了位点突变特征和非编码区序列在生物体的进化过程中往往具有重要的作用。

关键词: 木兰科, 叶绿体基因组, 密码子使用, 系统进化树