Characteristics and codon usage bias of Picea brachytyla var. complanata chloroplast genome

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.