[Codon usage bias and phylogenetic analysis of chloroplast genomes of 60 Lilium species]

Lilium, an important monocot genus, demonstrates rich genetic resources and application value. Chloroplast genomics of Lilium is essential for elucidating the evolutionary mechanisms. To elucidate the molecular genetic characteristics and evolutionary patterns of Lilium species, we comprehensively analyzed the genomic characteristics and synonymous codon usage bias of 60 Lilium species (representing approximately 49.58% of the genus worldwide). The results revealed that the 60 Lilium chloroplast genomes exhibited the average GC content of 37.00%, with GC content at the third codon position (GC₃) averaging 29.70%, indicating pronounced bias for AT bases. The average effective number of codons (ENC) ranged from 47.76 to 48.57, suggesting weak codon usage bias. Through ENC-GC_3s analysis and PR2 analysis, we determined that codon usage bias in Lilium chloroplast genomes was influenced by mutation pressure and natural selection, with natural selection playing a predominant role. Simple sequence repeat (SSR) analysis identified 5 750 SSRs, which were mainly distributed in intergenic spacer (IGS) regions and intron regions. Mononucleotide repeats, with A/T repeats being dominant, accounted for the highest proportion (41.91%), further explaining the A/T enrichment characteristic in the genome. Collinearity analysis showed that the gene arrangement patterns of Liliaceae species were similar, with only slight differences in the inverted repeat boundaries. Phylogenetic analysis based on chloroplast genome sequences of 158 Liliaceae species revealed that Lilium species formed a monophyletic clade, which was generally consistent with the existing taxonomic system, elucidating the phylogenetic relationships within the genus. This study provides comprehensive insights into the codon usage characteristics of Lilium chloroplast genomes at the molecular level, offering a theoretical foundation and data support for phylogenetic studies, molecular marker development, and chloroplast genetic engineering in Lilium. These findings have significant implications for the conservation and utilization of Lilium genetic resources.