Maize Genomics and Genetics 2024, Vol.15, No.4, 191-203 http://cropscipublisher.com/index.php/mgg 194 Observational methods, such as the analysis of plastome diversity within Zeamays, are also crucial. By examining the complete plastomes of South American maize landraces and teosintes, researchers identified polymorphic plastome loci and inferred evolutionary relationships among haplotypes. This study highlighted the importance of intraspecific plastome variation in understanding evolutionary processes at low taxonomic levels (López et al., 2021). A combination of molecular biology techniques, bioinformatics analysis, and experimental and observational methods provides a comprehensive toolkit for studying microstructural changes in the plastid genome of Zea. These approaches offer valuable insights into the evolutionary dynamics and functional implications of these changes, contributing to researchers understanding of plant genome evolution. 4 Microstructural Changes in the Zea Plasmid Genome 4.1 Changes in genome size and content The plastid genomes (plastomes) of Zea species exhibit notable variations in size and content. A comprehensive study on the genus Zea, which includes species such as Zea mays, Zea diploperennis, Zea perennis, Zea luxurians, and Zea nicaraguensis, revealed significant differences in genome size among these species. The study sequenced four complete plastomes and a nearly complete plastome, identifying 193 insertion or deletion mutations (indels) and 15 inversions across the examined plastomes (Orton et al., 2017). These microstructural changes contribute to the overall variation in genome size and content within the genus. Additionally, the plastid genome of Zeamays has been shown to undergo changes during different developmental stages. For instance, the plastid DNA (ptDNA) in maize seedlings transitions from large, intact molecules in proplastids to fragmented forms in photosynthetically active chloroplasts. This fragmentation process does not alter the overall genome sequence but results in variations in the physical state of the ptDNA (Figure 1) (Tripathi et al., 2022). These findings highlight the dynamic nature of plastid genome size and content in Zea species. 4.2 Changes in gene arrangement and repeat sequences The arrangement of genes and the presence of repeat sequences in the plastid genome of Zea species are subject to significant alterations. In the genus Zea, tandem repeat indels were identified as the most common type of microstructural change, indicating a high frequency of repeat sequence variations (Orton et al., 2017). These changes in repeat sequences can impact the stability and function of the plastid genome. Moreover, the loss of inverted repeat (IR) regions, which are crucial for genome stability, has been observed in other plant lineages and can provide insights into the evolutionary dynamics of Zea plastomes. For example, the loss of IR regions in conifer plastomes has been associated with changes in the selection pressure and substitution rates of protein-coding genes (Ping et al., 2022). Although this specific phenomenon has not been documented in Zea, it underscores the potential impact of IR region variations on plastid genome evolution. 4.3 Gene loss and acquisition in the plastid genome Gene loss and acquisition are critical aspects of plastid genome evolution in Zea species. The study of plastid genomes in the genus Zea revealed that certain genes are retained or lost at different rates across species. For instance, the nuclear gene iojap in Zea mays conditions a permanent deficiency in plastid differentiation, leading to the loss of ribosomes and high molecular weight RNA in affected plastids (Walbot and Coe, 1979). This gene loss can have profound effects on plastid function and overall plant development. In addition, the evolutionary history of plastid genomes in other plant lineages provides valuable insights into gene loss and acquisition in Zea. For example, the plastid genomes of parasitic plants in the Scrophulariaceae and Orobanchaceae families have experienced extreme reductions in gene content, with the loss of photosynthetic genes and the retention of translational genes like rps2 (dePamphilis et al., 1997). These patterns of gene loss and retention can inform our understanding of similar processes in Zea plastomes. Furthermore, the complete plastome sequences of seven species in the Gentiana sect. Kudoa revealed significant gene loss, particularly in the ndh gene family, which is involved in photosynthesis (Sun et al., 2018). This gene
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