Regardless of having identical photosynthetic pathways, chloroplast genomes vary depending on whether the host plant is monocotyledonous or dicotyledonous

The comprehension of the evolutionary mechanisms behind chloroplasts is derived from the comparative analysis of chloroplast (CP) genomes across various species. It sheds light on implementing molecular modifications and enhancing the efficacy of chloroplasts. In this study, we classified the chloroplast genomes of 12 organisms into monocots, dicots, and two C₃ and C₄ subgroups. Groups are as follows: 1. Dicots, C₃; 2. Dicots, C₄; 3. monocot, C₄; and 4. monocot and C₃. Following that, we conducted a comparative genomic analysis. Despite having differing mechanisms for carbon fixation, our findings revealed that there is 82% gene organization similarity between the dicot and monocot groups. In comparison, the estimated values for the C₄ and C₃ groups were 62% and 57%, respectively. The variation across the four groups is the result of several chromosomal rearrangements, particularly in the 9000 to 36,000 bp of the CP genomes. Additionally, GC content comparisons among the groups revealed that monocots have a greater GC content than dicots. We also discovered that 81% of simple sequence repeats were located in non-coding areas. Finally, our findings indicated that the amino acids in CP proteomes generally follow an identical pattern, particularly codons that follow a similar pattern for RSCU in all CP genomes. To summarize, our finding demonstrated that the assessment of CP genomes is a prerequisite for genetic modification and horizontal transfer of chloroplast genomes between plant species.