The tribe Ampelopsideae plants are important garden plants with both medicinal and ornamental values. The study of codon usage bias (CUB) facilitates a deeper comprehension of the molecular genetic evolution of species and their adaptive strategies. The joint analysis of CUB in chloroplast genomes (cpDNA) offers valuable insights for in-depth research on molecular genetic evolution, biological resource conservation, and elite breeding within this plant family. The base composition and codon usage preferences of the eighteen chloroplast genomes were highly similar, with the GC content of bases at all positions of their codons being less than 50%. This indicates that they preferred A/T bases. Their effective codon numbers were all in the range of 35–61, which indicates that the codon preferences of the chloroplast genomes of the 18 Ampelopsideae plants were relatively weak. A series of analyses indicated that the codon preference of the chloroplast genomes of the 18 Ampelopsideae plants was influenced by a combination of multiple factors, with natural selection being the primary influence. The clustering tree generated based on the relative usage of synonymous codons is consistent with some of the results obtained from the phylogenetic tree of chloroplast genomes, which indicates that the clustering tree based on the relative usage of synonymous codons can be an important supplement to the results of the sequence-based phylogenetic analysis. Eventually, 10 shared best codons were screened on the basis of the chloroplast genomes of 18 species. The codon preferences of the chloroplast genome in Ampelopsideae plants are relatively weak and are primarily influenced by natural selection. The codon composition of the chloroplast genomes of the eighteen Ampelopsideae plants and their usage preferences were sufficiently similar to demonstrate that the chloroplast genomes of Ampelopsideae plants are highly conserved. This study provides a scientific basis for the genetic evolution of chloroplast genes in Ampelopsideae species and their suitable strategies.

Codon use bias is an important characteristic in the process of genetic information transmission of species. With the publication of the genome of C. panzhihuaensis, it is of great significance to investigate the codon use bias for understanding the genetic evolution of this species and for molecular breeding. In this study, Perl language and CodonW 1.4.2 software was used to systematically analyze the coding gene sequences of the C. panzhihuaensis genome, obtain the characteristics of codon use, and identify the sources of variation affecting codon use. The results showed that GC3s content, GCall content, and ENC value were 46.75%, 47.67%, and 52.8 respectively. As the first seed plant, the GC3 content of Cycas is similar to that of most gymnosperms and most dicotyledons, but considerably different from that of monocotyledons.RSCU value was greater than 1, among which 21 codons ended in U or A. Enc-plot analysis, PR2-plot neutral plot analysis, and correlation coefficient analysis of Axis1 with GC3s and CAI revealed that the codon bias was mainly affected by natural selection, but also by mutation pressure and other factors. Thirty-one optimal codons of Cycas genes were screened. This research can provide a reference for the phylogeny and genome codon evolution of Cycas.