Abstract: 　Codon W and EMBOSS were used to analyze the codon usage bias of PAL genes and possible formation mechanism from 42 different plant species, to provide theoretical guidance for the improvement of PAL gene expression in plants. RSCU results indicated that PAL genes from monocotyledonous plants had stronger codon usage bias than those from dicotyledons and other plants, with CUC as the optimal codon. PAL genes in monocotyledons prefer G/C codes, whereas PAL in dicotyledons prefer A/T codes. Enc-plot results showed that the codon usage bias of dicotyledons and other plants was mainly influenced by natural selection, while the codon usage bias of monocotyledons was influenced by both mutation and natural selection. Cluster analysis showed that CDS sequence-based clustering was more suitable than RSCU based clustering in phylogenetic analysis. The PAL genes of most monocotyledons were suitable for expression in E. coli, whereas the PAL genes of dicotyledons were suitable for expression in yeast. Furthermore, Arabidopsis thaliana might be the more appropriate genetic transformation receptor for genetic transformation of the PAL genes from 42 different plant species than tobacco. These results laid the theoretical foundation for genetic evolution investigation and functional validation of PAL genes.

Key words: Fritillaria, phenylalanine ammonia-lyase, codon usage bias, evolution analysis