Plant Gene and Traits 2024, Vol.15, No.3, 152-161 http://genbreedpublisher.com/index.php/pgt 154 synthetic allotetraploid Cucumis×hytivus and its diploid parents (C. hystrix and C. sativus) was sequenced and compared, revealing genetic variations such as indels and SNPs (Zhai et al., 2021). This analysis clarified the evolutionary and taxonomic position of C.×hytivus within the Cucumis subgenus. Similarly, the construction of a cucumber chloroplast pan-genome based on 121 cucumber germplasms identified three distinct phylogenetic groups: East Asian, Eurasian + Indian, and Xishuangbanna + Indian (Xia et al., 2023). Figure 1 presents a genetic variation and structure analysis of 50 cucumber chloroplast genomes, illustrating the nucleotide diversity and SNP-based phylogenetic relationships, which are crucial for understanding the genetic basis of species differentiation and breeding strategies within the Cucumis genus. Figure 1 Genetic variation and structure analysis of 50 cucumber chloroplast genomes (Adopted from Xia et al., 2023) Image caption: (a) Statistics of nucleotide diversity (Pi) in 50 cucumber chloroplast genomes with parameters of a window length of 1 000 bp and a step size of 100 bp. (b) The variations in 50 cucumber chloroplast genomes. The phylogenetic tree (c) and population structure analyses (d) are based on SNP (Adopted from Xia et al., 2023) 3.3 Comparison of chloroplast-derived phylogenetic trees with nuclear genomic data Comparing phylogenetic trees derived from chloroplast genomes with those based on nuclear genomic data can provide a more comprehensive understanding of plant evolution and taxonomy. Chloroplast genomes, being maternally inherited and highly conserved, often reveal different evolutionary patterns compared to nuclear genomes, which undergo biparental inheritance and recombination. For instance, in the study of the synthetic allotetraploid Cucumis×hytivus, chloroplast genome analysis supported maternal inheritance and provided insights into cytonuclear evolution (Zhai et al., 2021). In contrast, nuclear genomic studies might focus on different aspects of genetic variation and evolutionary history. The integration of both chloroplast and nuclear genomic data can help resolve discrepancies and provide a more robust phylogenetic framework. For example, in the case of the cucumber, chloroplast genome analysis revealed distinct phylogenetic groups, while nuclear genomic studies might further elucidate the genetic basis of these groupings and their evolutionary significance (Xia et al., 2023). 4 Taxonomic Implications of Chloroplast Genomic Studies 4.1 Resolving taxonomic discrepancies in the Cucumis genus using chloroplast DNA Chloroplast DNA (cpDNA) has proven to be a valuable tool in resolving taxonomic discrepancies within various plant genera, including Cucumis. The comparative analysis of chloroplast genomes can reveal significant genetic variations that are not apparent through morphological studies alone. For instance, the study on the synthetic allotetraploid Cucumis×hytivus and its diploid parents demonstrated that chloroplast genomes can clarify
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