Maize Genomics and Genetics 2024, Vol.15, No.4, 191-203 http://cropscipublisher.com/index.php/mgg 192 2 Evolutionary Background of Zea Plastids 2.1 Historical evolution of Zea The genus Zea, which includes the well-known species Zea mays (maize), has a rich evolutionary history that is intricately linked to its plastid genome. The plastid genome, or plastome, of Zea species has been a focal point of evolutionary studies due to its relatively stable inheritance and the critical role it plays in photosynthesis and other cellular functions. The historical evolution of Zea can be traced back to its divergence from a common ancestor with other grasses. The stem lineage of all Zea species was calculated to have diverged approximately 176 000 years before present (YBP) (Orton et al., 2017). This divergence set the stage for the evolution of various Zea species, each adapting to different ecological niches and undergoing unique microstructural changes in their plastomes. 2.2 Phylogenetic context Phylogenetic analyses have been instrumental in understanding the evolutionary relationships within the genus Zea. Complete plastome sequences from multiple Zea species, including Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis, have been used to construct phylogenetic trees that reveal the rates and patterns of microstructural changes such as inversions and insertion or deletion mutations (indels) (Orton et al., 2017). These analyses have confirmed the close relationships among Zea species and have provided insights into the divergence times of specific nodes within the genus. For instance, divergence dates for specific nodes relative to Zea were estimated to fall between 38 000 YBP for certain subspecies and 23 000 YBP for the section Luxuriantes (Orton et al., 2017). The phylogenetic context of Zea plastids is further enriched by studies on nuclear ribosomal internal transcribed spacer (ITS) sequences, which have been used to evaluate patterns of concerted evolution and substitution rates among Zea taxa (Buckler and Holtsford, 1996). These studies have identified significant differences in ITS substitution rates among Zea species, highlighting the role of selection in shaping the observed polymorphisms and substitutions. 2.3 Genetic divergence Genetic divergence within the genus Zea is marked by a variety of microstructural changes in the plastid genome. A comprehensive study identified 193 indels and 15 inversions across the examined plastomes of Zea species, with tandem repeat indels being the most common type of microstructural change observed (Orton et al., 2017). These changes are not uniformly distributed, indicating that different Zea species have undergone unique evolutionary paths despite their close relationships. The genetic divergence of Zea plastids is also reflected in the response to polyploidization, a process that has played a significant role in the evolutionary history of many eukaryotic species, including Zea mays. Polyploidization often leads to large-scale genomic reorganizations and phenotypic alterations. Studies have shown that different Zea mays inbred lines exhibit varying morphological responses to changes in ploidy, demonstrating the existence of genetic variation for the response to ploidy change within the species (Riddle et al., 2006). Moreover, the plastome diversity within Zea mays has been explored through the sequencing of complete plastomes from various South American maize landraces and teosintes. These analyses have identified a total of 124 polymorphic plastome loci, which have been used to infer evolutionary relationships among haplotypes and to understand the phylogeographic structuring of maize landraces . The structuring of haplotype diversity in these landraces reflects the distinction between Andean and South American lowland gene pools, providing further insights into the genetic divergence within Zeamays. The evolutionary background of Zea plastids is characterized by a complex interplay of historical divergence, phylogenetic relationships, and genetic divergence. The plastid genome of Zea species has undergone significant microstructural changes, which have been shaped by various evolutionary forces, including selection, polyploidization, and geographic structuring. These insights not only enhance our understanding of the
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