Maize Genomics and Genetics 2024, Vol.15, No.5, 218-227 http://cropscipublisher.com/index.php/mgg 218 Systematic Review Open Access Phylogenomic Studies in Zea: Evolutionary Relationships and Species Divergence Jiansheng Li Sanya Institute of China Agricultural University, Sanya, 572025, Hainan, China Corresponding email: lijiansheng@cau.edu.cn Maize Genomics and Genetics, 2024, Vol.15, No.5 doi: 10.5376/mgg.2024.15.0021 Received: 08 Jul., 2024 Accepted: 15 Aug., 2024 Published: 06 Sep., 2024 Copyright © 2024 Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li J.S., 2024, Phylogenomic studies in zea: evolutionary relationships and species divergence, Maize Genomics and Genetics, 15(5): 218-227 (doi: 10.5376/mgg.2024.15.0021) Abstract Phylogenomic studies have significantly advanced our understanding of the evolutionary relationships and species divergence within the genus Zea. By analyzing complete plastid genomes from five Zea species (Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis), this study investigates the rates and patterns of microstructural changes, including inversions and insertion/deletion mutations (indels). The findings reveal 193 indels and 15 inversions, with tandem repeat indels being the most prevalent. Divergence times were estimated using a noncorrelated relaxed clock method, indicating that the stem lineage of all Zea species diverged approximately 176 000 years before present (YBP). The mutation rates for the genus ranged from 1.7E-8 to 3.5E-8 microstructural changes per site per year, highlighting non-uniform rates of change despite close taxonomic relationships. These results corroborate previous studies on Zea mitochondrial and nuclear data, providing a comprehensive phylogenomic framework for understanding the evolutionary history and diversification of Zeaspecies. Keywords Maize (Zeamays); Phylogenomics; Zeaspecies; Microstructural changes; Divergence times; Plastid genomes 1 Introduction The genus Zea, belonging to the grass family Poaceae, is of significant agronomic and scientific importance. It includes several species, with maize (Zeamays) being the most prominent. Maize is not only a staple food crop but also a model organism for genetic and genomic research due to its extensive genetic diversity and well-characterized genome (Strable and Scanlon, 2009; Vincent, 2012). The genus Zea also includes wild relatives known as teosintes, which are crucial for understanding the evolutionary history and domestication of maize (Dermastia et al., 2009; Hufford et al., 2012a). The evolutionary study of Zea provides insights into plant domestication, adaptation, and the genetic basis of important agronomic traits (Kellogg and Birchler, 1993; Hilton and Gaut, 1998). Phylogenomics, the intersection of phylogenetics and genomics, is a powerful tool in evolutionary biology. It involves the analysis of genome-wide data to infer evolutionary relationships and understand the genetic basis of phenotypic diversity (Kellogg and Birchler, 1993). In the context of Zea, phylogenomic studies have elucidated the evolutionary relationships among different species and subspecies, shedding light on the processes of speciation and domestication (Hilton and Gaut, 1998; Ross-Ibarra et al., 2009). These studies are crucial for understanding the genetic mechanisms underlying important traits such as disease resistance, yield, and environmental adaptability (Strable and Scanlon, 2009; Mounika et al., 2018). By integrating phylogenetic and genomic data, researchers can gain a comprehensive understanding of plant evolution and the factors driving genetic diversity (Kellogg and Birchler, 1993; Curry 2020). This study investigates the evolutionary relationships within the genus Zea using phylogenomic approaches. This includes understanding the divergence times, gene flow, and adaptive evolution among different Zea species and subspecies. The study aims to contribute to the broader field of plant science by providing insights into the genetic basis of important agronomic traits and the evolutionary processes shaping plant diversity. Additionally, this research will inform conservation strategies for wild relatives of maize and guide breeding programs aimed at improving crop resilience and productivity.
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