Characterization of the chloroplast genome and phylogenetic analysis of Pyropia ishigecola (Bangiales, Rhodophyta)

this study reports the first complete chloroplast genome of P. ishigecola, providing key insights into its genomic features, codon usage patterns, selective pressures, and phylogenetic relationships. Comparative analyses reveal conserved gene structures interspersed with variable intergenic regions, while collinearity patterns highlight the retention of ancestral rDNA operons. Codon usage bias is primarily shaped by selective forces, with implications for gene expression and adaptation. Positive selection detected in several energy-related genes (atpA, rpoA) suggests a role in environmental acclimation. Furthermore, the use of whole chloroplast genomes significantly improves phylogenetic resolution compared to traditional single-gene approaches, offering a robust framework for future evolutionary and systematic studies within Pyropia and related genera.