Objective To analyze the codon bias of PmDXR gene in Pinus massoniana in order to provide a theoretical basis for the subsequent functional verification and genetic transformation of PmDXR gene.

Method The codon bias of DXR gene of P. massoniana and other 37 species was analyzed by CodonW, EMBOSS and SPSS online program. Neutral analysis, PR2-plot analysis and ENC-plot analysis were conducted to speculate the main factors for the formation of DXR gene codon bias. Then the codon frequency of the PmDXR gene of P. massoniana were compared with those of the 4 model organisms’ genome codon usage bias.

Result The results showed that the codon bias level of PmDXR was low and biased toward the synonymous codons with A or T. The DXR codon bias analysis of different species showed that different species had different codon preference patterns, and gymnosperms DXR genes had stronger codon preference than angiosperm. The CDS sequences and RSCU cluster analysis showed that the preference of PmDXR gene was similar to other gymnosperms. Neutral analysis, PR2-plot analysis and ENC-plot analysis results indicated that the codon bias of DXR gene was mainly affected by natural selection. The codon usage frequency comparison and analysis showed that eukaryotic expression system of yeast was more suitable for heterologous expression of PmDXR gene in the selection of heterologous transforming receptors. The model plants Arabidopsis thaliana and Nicotiana tabacum can be used as genetic transformation receptors for PmDXR gene, but N. tabacum is the most ideal genetic transformation receptor.

Conclusion This study initially revealed the codon preference of the PmDXR gene, the results provides an important guidance for the subsequent gene function verification, and also provides a scientific basis for the study of molecular evolution of P. massoniana.