Plant Gene and Traits 2024, Vol.15, No.3, 152-161 http://genbreedpublisher.com/index.php/pgt 153 within the Cucumis genus by investigating genetic variations and evolutionary patterns in their chloroplast genomes, with a particular focus on hybridization and polyploidization events. 2 Chloroplast Genome Structure and Features 2.1 General structure and function of chloroplast genomes in plants Chloroplast genomes in plants are typically circular DNA molecules that are highly conserved across different species. They generally exhibit a quadripartite structure, which includes a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Niu et al., 2023; Xia et al., 2023; Xin et al., 2023). The size of chloroplast genomes can vary, but they usually range from approximately 150 000 to 170 000 base pairs (bp) (Liang et al., 2020). These genomes encode essential genes for photosynthesis and other metabolic processes, including protein-coding genes, transfer RNA (tRNA) genes, and ribosomal RNA (rRNA) genes (Abdullah et al., 2020). The conserved nature of chloroplast genomes makes them valuable tools for studying plant phylogeny, species identification, and evolutionary relationships (Wang et al., 2023). 2.2 Specific characteristics of chloroplast genomes inCucumis species The chloroplast genomes of Cucumis species, such as cucumber (Cucumis sativus), exhibit typical quadripartite structures with sizes ranging from approximately 154 673 to 157 641 bp. These genomes consist of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeats (IRs) (Zhai et al., 2021). Comparative genomic analyses have revealed significant genetic variation within the chloroplast genomes of different Cucumis species, particularly between Indian ecotype cucumbers and other cultivars. This genetic diversity is crucial for understanding the evolutionary history and adaptation mechanisms of Cucumis species. Additionally, studies have shown that chloroplast genes in Cucumis species respond to environmental stresses, such as temperature changes, by regulating lipid metabolism and ribosome metabolism (Xia et al., 2023). 2.3 Advances in sequencing technologies for chloroplast genomes Advances in sequencing technologies, particularly next-generation sequencing (NGS), have revolutionized the study of chloroplast genomes. NGS allows for the rapid and accurate assembly of complete chloroplast genomes, facilitating comparative genomic analyses and phylogenetic studies (Liang et al., 2020; Song et al., 2022). The use of NGS has enabled researchers to sequence and characterize the chloroplast genomes of numerous plant species, including those within the Cucumis genus. These technologies have also made it possible to identify hypervariable regions and simple sequence repeats (SSRs) within chloroplast genomes, which can serve as molecular markers for species identification and genetic diversity studies. The increasing availability of complete chloroplast genome sequences in public databases has further enhanced our understanding of chloroplast genome evolution and its implications for plant taxonomy and phylogeny (Zhou et al., 2021). 3 Phylogenetic Analysis Using Chloroplast Genomes 3.1 Techniques for chloroplast genome-based phylogenetic studies Chloroplast genome-based phylogenetic studies leverage the highly conserved nature of chloroplast DNA (cpDNA) to infer evolutionary relationships among plant species. Techniques commonly used include whole chloroplast genome sequencing, comparative genomic analysis, and the identification of hypervariable regions that serve as molecular markers. For instance, sequencing and comparative analysis of chloroplast genomes have been employed to study genetic variations and evolutionary relationships in various plant species, such as Cucumis, Cleomaceae, and Mangifera (Alzahrani et al., 2021; Zhai et al., 2021). These studies often involve the assembly of complete chloroplast genomes, annotation of genes, and the use of phylogenetic trees constructed through methods like maximum likelihood (ML) and Bayesian Inference (BI) (Liu et al., 2021; Xin et al., 2023). Additionally, the identification of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) within the chloroplast genome can provide further insights into genetic diversity and phylogenetic relationships (Li et al., 2020). 3.2 Phylogenetic relationships within the Cucumis genus based on chloroplast DNA Phylogenetic analysis within the Cucumis genus using chloroplast DNA has revealed significant insights into the evolutionary relationships and taxonomic positions of various species. For example, the chloroplast genome of the
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