Plant Gene and Traits 2024, Vol.15, No.3, 152-161 http://genbreedpublisher.com/index.php/pgt 155 evolutionary and taxonomic positions by identifying specific genetic variations such as Indels and SNPs (Zhai et al., 2021). Similarly, the identification of mutational hotspots and highly polymorphic regions in other genera, such as Artemisia and Abelmoschus, has been instrumental in resolving taxonomic ambiguities and inferring phylogenetic relationships (Li et al., 2020; Shahzadi et al., 2020). These findings underscore the potential of cpDNA in addressing taxonomic challenges within the Cucumis genus. 4.2 Chloroplast genome markers for species identification and classification Chloroplast genome markers are essential for species identification and classification due to their high resolution and specificity. In the genus Chenopodium, for example, the development of species-specific molecular markers based on InDels and SNPs has enabled the precise identification of closely related species (Wei et al., 2023). Similarly, in the genus Abelmoschus, mutational hotspots such as start-psbA and atpB-rbcL have been identified as potential markers for resolving taxonomic discrepancies (Li et al., 2020). Figure 2 illustrates the chloroplast genome map of three Abelmoschus species, highlighting the organization of genes within the chloroplast genome and their transcriptional orientation, which provides a comparative framework for understanding the chloroplast genome structures across different plant genera. These markers are particularly useful in distinguishing species with high morphological similarity, as demonstrated in the study of Lespedeza species, where complete chloroplast genomes provided unique molecular features for accurate species identification (Somaratne et al., 2019). The application of such markers in the Cucumis genus could significantly enhance the accuracy of species classification and identification. Figure 2 Chloroplast genome map of three Abelmoschus species (Adopted from Li et al., 2020) Image caption: Genes shown outside the circle are transcribed clockwise and those inside counterclockwise. Genes belonging to different functional groups are color-coded (Adopted from Li et al., 2020) 4.3 Implications of chloroplast genomics for understanding speciation and divergence Chloroplast genomics offers profound insights into the processes of speciation and divergence. The study of chloroplast genomes in the Zingiberaceae family revealed that hybridization events within related groups could explain the complex phylogeny observed in these species (Liang et al., 2020). This highlights the role of chloroplast DNA in tracing evolutionary histories and understanding the mechanisms of speciation. In the case of Cucumis, the comparative analysis of chloroplast genomes between allotetraploid and diploid species provided
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