Plant Gene and Traits 2024, Vol.15, No.3, 152-161 http://genbreedpublisher.com/index.php/pgt 152 Feature Review Open Access Application of Chloroplast Genomes in Phylogenetic and Taxonomic Studies of the Cucumis Genus Wenzhong Huang, Zhongmei Hong CRO Service Station, Sanya Tihitar SciTech Breeding Service Inc., Sanya, 572025, Hainan, China Corresponding email: zhongmei.hong@hitar.org Plant Gene and Trait, 2024, Vol.15, No.3 doi: 10.5376/pgt.2024.15.0016 Received: 19 May, 2024 Accepted: 21 Jun., 2024 Published: 30 Jun., 2024 Copyright © 2024 Huang and Hong, 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: Huang W.Z., and Hong Z.M., 2024, Application of chloroplast genomes in phylogenetic and taxonomic studies of the Cucumis genus, Plant Gene and Trait, 15(3): 152-161 (doi: 10.5376/pgt.2024.15.0016) Abstract This study explores the application of chloroplast genomes in addressing phylogenetic and taxonomic challenges within the Cucumis genus. Chloroplast genomes, due to their conserved nature and maternal inheritance, provide valuable genetic markers for elucidating evolutionary relationships and resolving taxonomic ambiguities. The complete sequencing of chloroplast genomes from various Cucumis species, including synthetic allotetraploids like Cucumis×hytivus, has revealed significant genetic variations such as indels and SNPs that clarify species' evolutionary positions. Comparative genomic studies have also identified hypervariable regions and mutational hotspots within chloroplast DNA, which are essential for species identification and understanding adaptive evolution. Integrating chloroplast genomic data with nuclear and mitochondrial genomes has proven effective in constructing robust phylogenetic frameworks and resolving deep phylogenetic nodes. Furthermore, these genomic insights have practical applications in breeding programs, where they aid in developing new cultivars with desirable traits. Future research should focus on expanding chloroplast genome sequencing across a broader range of Cucumis species and employing advanced genomic technologies to enhance phylogenetic resolution and understand the genus's evolutionary history comprehensively. Keywords Cucumis; Chloroplast genomes; Phylogenetics; Taxonomy; Genetic markers 1 Introduction The Cucumis genus, belonging to the Cucurbitaceae family, encompasses a variety of species that are of significant economic and botanical importance. This genus includes well-known crops such as cucumbers (Cucumis sativus) and melons (Cucumis melo), which are cultivated worldwide for their nutritional and economic value. Cucumis species are not only vital for human consumption but also play a crucial role in agricultural systems due to their diverse uses and adaptability to different climatic conditions. The genus is characterized by a wide range of morphological diversity, which has led to challenges in its taxonomic classification and phylogenetic relationships (Zhai et al., 2021; Xia et al., 2023). Chloroplast genomes (cp genomes) have emerged as powerful tools in phylogenetic and taxonomic studies due to their highly conserved nature and maternal inheritance. The cp genome provides valuable molecular markers that can be used to resolve phylogenetic relationships and clarify taxonomic ambiguities within and among plant species (Fučíková et al., 2016; Somaratne et al., 2019). The comparative analysis of cp genomes allows for the identification of mutational hotspots, simple sequence repeats (SSRs), and other genetic variations that are crucial for species identification and evolutionary studies (Li et al., 2020; Alzahrani et al., 2021). In the context of the Cucumis genus, cp genomes have been instrumental in understanding the genetic and evolutionary dynamics, especially in complex scenarios such as allopolyploidization (Zhai et al., 2021; Xia et al., 2023). The aim of this study is to explore the application of chloroplast genomes in addressing phylogenetic and taxonomic challenges within the Cucumis genus. By leveraging the complete chloroplast genome sequences, this study aims to clarify the phylogenetic relationships among Cucumis species, including those with complex genetic backgrounds, by constructing robust phylogenetic trees based on chloroplast genome data. Additionally, it seeks to resolve taxonomic ambiguities by identifying and analyzing genetic markers within the chloroplast genomes that can aid in the accurate classification and differentiation of Cucumis species, thereby addressing existing taxonomic discrepancies. Furthermore, the study aims to enhance our understanding of the evolutionary dynamics
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