Codon usage patterns and phylogenetic analysis of chloroplast genomes reveal evolutionary insights into Asphodelaceae species.

The phenomenon of codon usage bias (CUB) is prevalent across various genomes and offers critical insights into the molecular genetic evolution of organisms, as well as their adaptive strategies. Comparative analyses of CUB in chloroplast (cp.) genomes further deepen our understanding of the intricate phylogenetic relationships across taxonomic groups. The Asphodelaceae family, a globally distributed plant group with significant ecological and economic value, has been extensively applied in traditional medicine, landscape beautification, and nutritional supplementation. In this study, we systematically analyzed the codon usage patterns and phylogenetic relationships of 13 diverse Asphodelaceae species based on their cp. genomes. Our findings indicated that both base composition and codon usage preferences were highly similar among the 13 cp. genomes examined. The Asphodelaceae species displayed a pronounced bias toward A/T-rich nucleotides and A/T-ending codons; notably, the corresponding values of the effective number of codons (ENC) were in the range of 35–61, indicative of a relatively weak CUB in this family. Each species contained 30 identical high-frequency codons and 13–18 individual optimal codons, presenting a striking prevalence of terminating in A/T nucleotides. The findings from the ENC plot, neutrality plot, and parity rule 2 plot analyses augmented the inference that both natural selection and mutation pressure exert influence on the codon usage patterns of Asphodelaceae species. Correlation analysis indicated a significant association between codon bias indicators and genomic nucleotide composition (particularly GC3), suggesting that compositional constraints correlate with and may underlie the observed CUB patterns. In addition, the genetic relationships inferred from the relative synonymous codon usage (RSCU) values were basically consistent with the phylogenetic topology derived from the cp. protein-coding genes. All taxa within the studied genera of the Asphodelaceae family exhibited strong phylogenetic clustering, thereby confirming that species with closer evolutionary relationships tend to share more similar codon usage preferences. This finding illustrates that RSCU-based clustering analysis can effectively supplement sequence-based phylogenetics in elucidating evolutionary relationships among species at the family level. The CUB of cp. genomes in Asphodelaceae plants is relatively weak and is subject to the combined effects of multiple factors. All taxa within the studied genera of the Asphodelaceae family have been confirmed to be closely related to each other in terms of their evolutionary relationships as well as the codon usage patterns of their cp. genomes. This study elucidates the codon usage patterns of Asphodelaceae species and enhances the understanding of codon biology and genetic evolution across a diverse range of organisms.