Comparison between the codon preferences of the transcriptomes of Pinus kesiya and Pinus yunnanensis

The comparison of the codon usage patterns in the transcriptomes of Pinus kesiya and P. yunnanensis provided a basis for the codon modification of hetero-expression of P. kesiya genes.

In the present study, the codon base composition and other relative parameters of the transcriptomes of P. kesiya and P. yunnanensis were analyzed and calculated using Codon W 1.4.2, and the optimal codon was deduced and compared with the codon usage frequency of other fungus and plants.

The base composition of the transcriptome of P. yunnanensis was GC12 (0.50) > GC3s (0.47), and the composition of the P. kesiya transcriptome was GC12 (0.51) > GC3s (0.32). In terms of the base composition of the transcriptomes of different tissues, the high-resin bark was in the order of GC12 (0.49) > GC3s (0.45), and the low-resin bark was in the order of GC12 (0.50) > GC3s (0.41), which illustrated that their codons all preferred AU at the third base of the transcriptome of different tissues of P. yunnanensis and P. kesiya. All their CAI values were relatively lower than those of angiosperms, indicating the transcriptome codon preference of different tissues of P. yunnanensis and P. kesiy. The neutrality plot and ENC-plot analysis indicated that their usage patterns were mainly affected by selection pressures. The optimal codons had a small difference between the transcriptome of different tissues of P. kesiya and P. yunnanensis. The codon usage frequency of P. kesiya, P. yunnanensis, Arabidopsis thaliana, Populus trichocarpa, Aspergillus nidulans and Saccharomyces prombe was compared, and the results revealed that the codon preferences of P. kesiya and P. yunnanensis were pretty similar, which were relatively close to those of A. niger and A. thaliana, illustrating that the eukaryotic expression system of A. nidulans was more suitable for the heterologous expression of the P. kesiya genes.

The codon usage bias of the transcriptome coding sequences of P. yunnanensis and P. kesiya was mainly affected by selection and the joint action of many factors, and A. nidulans was the optimal heterologous expression receptor for P. kesiya genes. The present study has provided some scientific background and a theoretical basis for the transgenic breeding and hybridization breeding, heterologous expression of specific genes of P. kesiya and the improvement of the expression efficiency of exogenous genes.