Complete Chloroplast Genome Sequences of Three Species: Genome Characterization, Comparative Analyses, and Phylogenetic Relationships Within Zingiberales.

, the sole member of the Cannaceae family, is widely cultivated as an ornamental plant for its decorative flowers and foliage and is also a potential tuber crop due to its high starch content. This study sequenced, assembled, and analyzed the complete chloroplast (cp) genomes of three common species with distinct leaf colors (green, purple, and variegated). The four cp genomes ranged from 164,427 to 164,509 bp in length, had a GC content of 36.23-36.25%, and exhibited identical gene content and codon preferences. Each genome contained 130 genes, including 110 unique genes (78 protein-coding genes, four of unknown function, four rRNAs, and 28 tRNAs), 18 duplicated genes located in the IR regions (six protein-coding genes, two of unknown function, four rRNAs, and eight tRNAs), and two genes in the LSC region. SSR and long-repeat showed differences in long repeats numbers and distributions among the four cp genomes, highlighting potential molecular markers for species identification and breeding. Comparative analysis showed high conservation across cp genomes. Phylogenetic analysis confirmed a close relationship between Cannaceae and Marantaceae and supported a [Musaeceae (Cannaceae + Marantaceae)] clade as a sister group to Costaceae. The cp genome data generated in this study provide valuable insights for developing molecular markers, resolving taxonomic classifications, and advancing phylogenetic and population genetic studies in species.