为探究使君子科（Combretaceae）红树植物叶绿体基因组密码子使用偏好性及其影响因子，对拉关木（Laguncularia racemosa C. F. Gaertn.）、红榄李〔Lumnitzera littorea (Jack) Voigt〕、榄李（Lumnitzera racemosa Willd.）叶绿体基因组的52个共有蛋白质编码序列（CDS）进行密码子第1、第2、第3位碱基的GC含量（分别为GC₁、GC₂、GC₃）、密码子总GC含量（GC_all）、有效密码子数（ENC）和相对同义密码子使用度（RSCU）分析；在此基础上，对每种植物的GC₁、GC₂、GC₃、GC_all和ENC值进行相关性分析，并对每种植物叶绿体基因组进行中性绘图、ENC-plot、PR2-plot和最优密码子分析；此外，还基于rbcL基因序列和叶绿体基因组共有CDS的RSCU值对使君子科11种植物进行聚类分析。结果表明：3种植物叶绿体基因组GC_all值的均值为38.0%～38.2%，GC₁、GC₂和GC₃值的均值均低于50%，均表现为GC₁值的均值最大、GC₃值的均值最小，且GC₃值的均值明显低于GC₁和GC₂值的均值，并与二者呈不显著正相关；ENC值的均值为47.2～47.3，且3种植物叶绿体基因组中ENC值大于45的基因占比均高于70%。3种植物叶绿体基因组中的高频密码子均有29个，以A或U结尾的高频密码子占比达96.6%。中性绘图、ENC-plot和PR2-plot分析结果表明3种植物叶绿体基因组密码子使用偏好性主要受自然选择的影响。拉关木、红榄李和榄李叶绿体基因组的最优密码子分别有8、6和10个，且多以A或U结尾；共有最优密码子有4个，分别为CGA、AGA、GGA、ACA。聚类分析结果表明红榄李和榄李均首先聚在一起，说明二者的亲缘关系较近。综上所述，3种红树植物叶绿体基因组密码子偏好以A或U结尾，且密码子使用偏好性主要受自然选择的影响。

To investigate the codon usage bias of chloroplast genomes of mangroves in Combretaceae and its affecting factors, GC contents of the first, second, and third bases of codon (GC₁, GC₂, and GC₃, respectively), total GC content of codon (GCall), effective number of codon (ENC), and relative synonymous codon usage (RSCU) of 52 common protein coding sequences (CDS) of chloroplast genomes of Laguncularia racemosa C. F. Gaertn., Lumnitzera littorea (Jack) Voigt, and Lumnitzera racemosa Willd. were analyzed; on the basis, the correlations between GC₁, GC₂, GC₃, GC_all, and ENC values of each species were analyzed, and neutral mapping, ENC-plot, PR2-plot, and optimal codon analyses were performed for chloroplast genomes of each species; in addition, cluster analysis was conducted for 11 species in Combretaceae based on rbcL gene sequences and RSCU values of common CDS of chloroplast genomes. The results show that the averages of GCall values of chloroplast genomes of the three species are 38.0%-38.2%, the averages of GC₁, GC₂, and GC₃ values are all lower than 50%, it is appeared in all of the three species that the average of GC₁ value is the largest and that of GC₃ value is the smallest, and the average of GC₃ value is obviously lower than those of GC₁ and GC₂ values and has non-significant positive correlations with them; the averages of ENC values are 47.2-47.3, and the percentages of genes with ENC value greater than 45 in chloroplast genomes of the three species are all greater than 70%. There are 29 high frequency codons in chloroplast genomes of the three species, and the high frequency codons ended with A or U account for 96.6%. The results of neutral mapping, ENC-plot, and PR2-plot analyses show that the codon usage bias of chloroplast genomes of the three species is mainly affected by natural selection. There are 8, 6, and 10 optimal codons in chloroplast genomes of Laguncularia racemosa, Lumnitzera littorea, and Lumnitzera racemosa, respectively, and most of them are ended with A or U; there are 4 common optimal codons, namely CGA, AGA, GGA, and ACA, respectively. The cluster analysis results show that Lumnitzera littorea and Lumnitzera racemosa are clustered together first, indicating that their relationship is close. In conclusion, the codons of chloroplast genomes of the three species of mangroves prefer to end with A or U, and the codon usage bias is mainly affected by natural selection.