Analysis of codon usage pattern in Lonicera × heckrottii ‘Gold Flame’ based on chloroplast genome

Abstract

Codon usage bias (CUB) was a unique feature of the genome, and revealing chloroplast genome codon usage bias can provide useful information for the evolution of plant species. Lonicera × heckrottii ‘Gold Flame’ is one of the members of the Lonicera genus with important ornamental value. However, the codon usage bias of chloroplast genome of this genotype has not been investigated. In this study, base compositions and various codon usage indices of 51 coding sequences from Lonicera × heckrottii ‘Gold Flame’ chloroplast genome was calculated, by Codon W, DnaSP, CUSP of EMBOSS and SPSS software. A total of 51 CDS of the Lonicera × heckrottii ‘Gold Flame’ chloroplast genome was selected to analyse codon usage bias. The results showed that the average GC content of 51 CDS sequences was 39.27%, and the average value of ENC was 48.75%. The chloroplast gene codon usage bias was weak, and preferred A/T ending. The general GC content order was GC1 (47.72%)>GC2 (39.89%)>GC3 (30.19%). Correlation analysis results showed that there was a significant positive correlation between GC content and GC1, GC2 and GC3 content. Combined with neutral plot analysis, ENC-plot and PR2-plot analysis, it is found that chloroplast gene codon usage preference was affected by mutations pressure and natural selection. In addition, the eight optimal codons in chloroplast genome were finally identified, codon bias ending with A/T. The study on the codon usage bias of Lonicera × heckrottii ‘Gold Flame’ provides a demonstration for exploring its genetic structure and molecular evolution mechanism, and provides a reference for molecular breeding.