Maize Genomics and Genetics 2024, Vol.15, No.4, 191-203 http://cropscipublisher.com/index.php/mgg 191 Feature Review Open Access Microstructural Changes in the Plastid Genome of Zea: Evolutionary Insights Liting Wang Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: liting.wang@hibio.org Maize Genomics and Genetics, 2024, Vol.15, No.4 doi: 10.5376/mgg.2024.15.0019 Received: 18 Jun., 2024 Accepted: 31 Jul., 2024 Published: 15 Aug., 2024 Copyright © 2024 Wang, 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: Wang L.T., 2024, Microstructural changes in the plastid genome of zea: evolutionary insights, Maize Genomics and Genetics, 15(4): 191-203 (doi: 110.5376/mgg.2024.15.0019) Abstract This study explores the evolutionary dynamics within the genus Zea by analyzing complete plastid genomes. The research sequenced plastomes from five Zea species, identifying 193 indels and 15 inversions, with tandem repeat indels being the most prevalent microstructural changes. Divergence times were estimated, revealing that the stem lineage of all Zea species diverged approximately 176 000 years before present (YBP), with mutation rates ranging from 1.7E-8 to 3.5E-8 changes per site per year. Additionally, the study examined plastome diversity within Zea mays, identifying 124 polymorphic loci and 27 distinct haplotypes, which reflect the geographic structuring of nuclear gene pools in South American maize landraces. The findings underscore the non-uniform rates of microstructural changes despite close taxonomic relationships and provide a comprehensive framework for understanding evolutionary processes at low taxonomic levels. This research contributes significantly to the phylogenomic knowledge of Zea, confirming previous mitochondrial and nuclear data analyses and highlighting the importance of plastid genome studies in elucidating evolutionary histories. Keywords Plastid genome; Zea evolution; Microstructural changes; Phylogenomics; Divergence times 1 Introduction Plastids are essential organelles in plant cells, originating from a photosynthetic bacterial endosymbiont. They possess their own genome, which has undergone significant reduction and rearrangement over evolutionary time (Barbrook et al., 2006; Rogalski et al., 2015). The plastid genome, or plastome, typically contains around 130 genes in higher plants, organized in a circular DNA molecule ranging from 100 to 220 kb in size (Rogalski et al., 2015). These genes are crucial for various cellular functions, including photosynthesis, transcription, and translation (Liebers et al., 2017). Plastids exhibit remarkable diversity, with different types such as chloroplasts, chromoplasts, and amyloplasts, each playing specific roles in plant development and metabolism (Liebers et al., 2017; Sierra et al., 2023). The evolution of plastid genomes provides critical insights into plant phylogeny and the adaptation of plants to different environments. The retention of plastid genomes in both photosynthetic and non-photosynthetic organisms highlights their essential roles beyond photosynthesis, such as in the synthesis of metabolic compounds and stress responses (Barbrook et al., 2006; Rogalski et al., 2015). Comparative analyses of plastid genomes across various plant species have revealed patterns of gene loss, retention, and rearrangement, which are key to understanding the evolutionary dynamics of these organelles (Huang et al., 2013; Yang et al., 2022). For instance, the study of plastid genomes in parasitic plants has shown how the loss of photosynthetic genes can lead to the retention of other essential genes, providing a model for genome degradation and adaptation (Krause, 2008; Graham et al., 2017). This study aims to explore the microstructural changes in the plastid genome of the genus Zea, focusing on evolutionary insights gained from these changes. By examining complete plastid genomes of various Zea species, including Zea mays and its congeneric species, this study seeks to identify and analyze the frequencies and types of microstructural changes such as inversions and indels. Additionally, the study will estimate divergence times and mutation rates within the genus, providing a comprehensive understanding of the evolutionary history and phylogenetic relationships among Zea species. This knowledge will contribute to broader discussions on plastid genome evolution and its implications for plant biology and biotechnology.
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