Maize Genomics and Genetics 2024, Vol.15, No.4, 191-203 http://cropscipublisher.com/index.php/mgg 198 6 Effects of Plastid Genome Changes on the Evolution of Zea Plants 6.1 Relationship with plant diversity The plastid genome, or plastome, plays a crucial role in the diversification of plant species, including those within the genus Zea. The study of plastid genomes across different Zea species has revealed significant microstructural changes, such as inversions and insertion or deletion mutations (indels), which contribute to genetic diversity. For instance, a comprehensive analysis of five Zea species identified 193 indels and 15 inversions, with tandem repeat indels being the most common type of microstructural change observed (Orton et al., 2017). These genetic variations are essential for understanding the evolutionary relationships and divergence times within the genus. The divergence dates for specific nodes relative to Zea were calculated to fall between 38 000 years before present (YBP) for the subspecies and 23 000 YBP for section Luxuriantes, with the stem lineage of all Zea species diverging at 176 000 YBP (Orton et al., 2017). The plastid genome's relatively low number of genes and its uniparental inheritance make it a valuable tool for phylogenetic studies. The gene content and genome rearrangements in plastids are efficient markers for capturing and understanding evolutionary events between different plant species (Rogalski et al., 2015). This genetic diversity within the plastid genome contributes to the overall diversity of the Zea genus, influencing traits such as morphology, physiology, and ecological adaptation. 6.2 Impact on plant adaptability Plastid genome changes significantly impact the adaptability of Zea plants to various environmental conditions. The plastid genome's role in photosynthesis and other metabolic processes is crucial for plant survival and adaptation. Structural rearrangements in the plastid genome, such as inversions and deletions, can lead to changes in gene expression and function, thereby affecting the plant's ability to adapt to different environments (Sugimoto et al., 2020). For example, the introduction of plastid-targeted restriction endonucleases in Arabidopsis resulted in various types of rearrangements in the plastid genome, leading to phenotypic changes such as leaf variegation and impaired chloroplast development (Sugimoto et al., 2020). These findings suggest that similar mechanisms could be at play in Zea plants, where plastid genome changes could enhance or impair adaptability. Moreover, the co-evolution of plastid and nuclear genomes plays a significant role in plant adaptability. The complex interactions between these genomes can result in plastome-genome incompatibilities, which can manifest as hybrid bleaching, hybrid variegation, or disturbances in the sexual phase (Greiner et al., 2011). These incompatibilities can act as barriers to hybridization, thereby influencing the adaptability and evolutionary trajectory of Zea plants. The ability of Zea plants to adapt to different environmental conditions is also influenced by the presence of stress-induced changes in chromosome and ploidy integrity, which can boost adaptive genome evolution in hostile environments (Storme and Mason, 2014). 6.3 Contribution to plant hybridization and speciation Plastid genome changes are instrumental in the processes of hybridization and speciation in Zea plants. The co-evolution of plastid and nuclear genomes can lead to cytonuclear genetic incompatibilities, which are crucial for reproductive isolation and speciation (Postel and Touzet, 2014). These incompatibilities can establish hybridization barriers, similar to the Dobzhansky-Muller model of speciation processes, thereby contributing to the formation of new species (Greiner et al., 2011). For instance, the study of plastid genomes in the genus Zea has shown that microstructural changes, such as indels and inversions, can influence the genetic compatibility between different species, affecting their ability to hybridize and form viable offspring (Orton et al., 2017). Hybridization and polyploidization are major evolutionary forces in plant evolution, including in Zea plants. The integration of nuclear and plastid genomic data has revealed that hybridization and polyploidization events are common in plant speciation (Karbstein et al., 2022). In the case of Zea, the presence of multiple hybrid origins involving different progenitor species and substantial post-origin evolution suggests that plastid genome changes play a significant role in the speciation process (Karbstein et al., 2022). Additionally, the study of plastid genomes in other plant groups, such as the inverted-repeat-lacking clade (IRLC) of legumes, has shown that plastid genome variation can provide insights into the mechanisms of genomic evolution and the potential for genetic
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