Codon usage bias of coding sequences has been usually used for exploring the evolutionary factors that affect the variation of genes. We took 20 chloroplast genomes of Malus species into account to explore the codon usage patterns, including the composition, relationship between GC3s and effective number of codons, the parity rule two analyses, the relative synonymous codon usage, the codon adaptation index, the frequency of optimal codons, the codon bias index, etc., of their coding genes. The relationship between GC3 and the ENC values showed that when the separate genes are concerned, the distribution of their GC3 contents is relatively concentrated and the distribution of the ENC values are from 35 to 61 or so. The neutrality plot showed that the correlation coefficient between GC12 and GC3 is 0.095, revealing the mutation factor played a weak role in codon pattern formation. Correspondence analysis results revealed that the codon usage patterns in the chloroplast genomes of Malus species are similar. All these results showed that all Malus chloroplast genomes are AT rich ones, the third bases of the codons are affected by the natural selection pressure, the first two nucleotide base of the codon are affected by mutation pressure. Some genes, such as the rsp7, psbA and ycf2 are of lower codon usage divergences, while the rps12, rps16 and ndhD are of higher codon usage divergences. Codon usage bias exists in the Malus genomes could be used for exploring the evolutionary characteristics in chloroplast genomes and for further study on evolutionary phenomenon in other species.

编码序列的密码子使用偏好通常被用于探索影响基因变异的进化因素。我们采集了海棠的 20 个叶绿体基因组考虑物种以探索密码子使用模式，包括组成、GC3 与有效密码子数之间的关系、奇偶规则二次分析、相对同义密码子使用、密码子适应指数、最佳密码子频率、密码子偏倚指数等，他们的编码基因。GC3与ENC值的关系表明，就分离基因而言，其GC3含量分布相对集中，ENC值分布在35~61之间。中性图显示GC12和GC3之间的相关系数为0.095，表明突变因子在密码子模式形成中起着微弱的作用。对应分析结果表明海棠叶绿体基因组密码子使用模式物种相似。综上所述，海棠叶绿体基因组均富含AT，密码子第三个碱基受自然选择压力影响，密码子前两个碱基受突变压力影响。一些基因，如rsp7、psbA和ycf2具有较低的密码子使用差异，而rps12、rps16和ndhD具有较高的密码子使用差异。海棠基因组中存在的密码子使用偏性可用于探索叶绿体基因组的进化特征，以及进一步研究其他物种的进化现象。