Maize Genomics and Genetics 2024, Vol.15, No.5, 218-227 http://cropscipublisher.com/index.php/mgg 224 Future prospects for using these technologies in Zea studies are promising. For instance, long-read sequencing could be employed to sequence the genomes of lesser-studied Zea species, thereby filling gaps in our current genomic databases and providing a more complete picture of the genus's evolutionary history (Orton et al., 2017). Additionally, CRISPR could be used to investigate the functional roles of specific genes identified through phylogenomic analyses, thereby enhancing researchers understanding of the genetic basis of key traits such as drought tolerance and disease resistance. 6.2 Integrating phylogenomics with other disciplines The integration of phylogenomics with other scientific disciplines such as ecology, physiology, and environmental science holds great potential for advancing researchers understanding of Zea evolution. By combining genomic data with ecological and physiological information, researchers can gain a more holistic view of how environmental factors and physiological adaptations have shaped the evolutionary trajectories of Zea species (Siepel, 2009; Fu et al., 2024). For example, ecological data on habitat preferences and environmental conditions can be used to contextualize phylogenomic findings, thereby providing insights into how different Zea species have adapted to their respective environments. Similarly, physiological studies on traits such as photosynthetic efficiency and water use can help elucidate the genetic basis of these adaptations and their evolutionary significance (Koenen et al., 2019). An interdisciplinary approach can also facilitate the identification of key genes and pathways involved in important traits, thereby informing breeding programs aimed at improving crop resilience and productivity. For instance, integrating phylogenomic data with physiological studies on drought tolerance could help identify candidate genes for genetic improvement, thereby contributing to the development of more resilient Zea varieties (Orton et al., 2017; McKain et al., 2018). 6.3 Addressing knowledge gaps Despite significant advances in Zea phylogenomics, several knowledge gaps remain. One major gap is the limited genomic data available for many Zea species, particularly those that are less economically important than Zea mays. This lack of data hampers researchers ability to construct comprehensive phylogenies and understand the full extent of genetic diversity within the genus (Orton et al., 2017; McKain et al., 2018). Another gap is the incomplete understanding of the evolutionary processes that have shaped the genetic diversity of Zea species. For instance, the roles of hybridization, introgression, and incomplete lineage sorting in Zea evolution are not fully understood and warrant further investigation (Vargas et al., 2017; Guo et al., 2022). Addressing these gaps will require the application of advanced genomic technologies and interdisciplinary approaches, as well as the generation of new genomic data for under-studied species. Proposed research directions to fill these gaps include the sequencing of additional Zea genomes using long-read technologies, which will provide more complete and accurate genomic data for phylogenetic analyses (Orton et al., 2017; McKain et al., 2018). Additionally, studies investigating the roles of hybridization and introgression in Zea evolution could provide valuable insights into the genetic mechanisms underlying species divergence and adaptation (Vargas et al., 2017). 7 Concluding Remarks The phylogenomic studies within the genus Zea have provided significant insights into the evolutionary relationships and species divergence. The analysis of complete plastid genomes (plastomes) across five Zea species revealed substantial microstructural changes, including 193 indels and 15 inversions, with tandem repeat indels being the most common. Divergence times were estimated, indicating that the stem lineage of all Zea species diverged approximately 176 000 years before present (YBP), with more recent divergence events occurring between 38 000 and 23 000 YBP. Additionally, the study confirmed previous findings from mitochondrial and nuclear data, reinforcing the robustness of the phylogenomic approach. Another study highlighted the role of gene flow in the evolutionary history of Zea, showing that gene flow has been a significant
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