This study was designed to analyze the codon usage bias and characteristics of the Picea brachytyla var. complanata chloroplast genome to provide a theoretical basis for the research of P. brachytyla.

The chloroplast genome of P. brachytyla was sequenced using the Illumina Hiseq platform. Using CodonW 1.4.2 and the online software CUSP, we performed analysis on the codons of the P. brachytyla chloroplast genes and explored the influencing factors for codon preference.

The cpDNA was a circular DNA molecule with a total length of 124,161bp. Unlike the typical chloroplast genome with a conserved quadripartite structure, the chloroplast genome of P. brachytyla exhibited a loss of inverted repeat regions, and the GC content was 38.7%. The genome contained 113 genes, including 76 protein-coding genes, 4 ribosomal RNA genes, and 33 transfer RNA genes. Further phylogenomic analysis showed that P. brachytyla and P. sitchensis were clustered in a unique clade in the Picea genus. The GC content at different locations of the cpDNA codons of P. brachytyla from low to high was GC₃ (49.39%) < GC₂ (40.73%) < GC₁(30.48%), indicating the last codon of the chloroplast genome favored A and U. 86% of the cpDNA coding genes had an ENC value above 45, indicating that the codon bias was weak. The correlation coefficient between GC₁₂ and GC₃ indicated no significant correlation(r=0.166 4, b=-0.157 7). The ratio of ENC frequency in the range of -0.05 to 0.05 was 57%, suggesting that the preference for the codon usage pattern of the chloroplast genome of P. brachytyla was mostly affected by selection and other factors. Most of the genes in the chloroplast genome of P. brachytyla were distributed in the lower part of the PR2 plan, namely, T > A and G > C, suggesting that the preference of the codon usage of the chloroplast genome of P. brachytyla was affected by selection and mutation factors. Finally, 12 codons such as UCU, AAA, GGU, GCA, GUU, UGU, UCC, CAU, GCU, CGU, GAA and AUU were determined as the optimal codons for the chloroplast genome of P. brachytyla.

The codon of P. brachytyla cpDNA prefers to use codons ending in A or U, which is mainly affected by selection and mutation.

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.