Cotton Genomics and Genetics 2024, Vol.15, No.2, 81-92 http://cropscipublisher.com/index.php/cgg 85 molecular phylogenetic analyses. For example, the evolutionary history and domestication of Gossypiumspecies, as revealed through molecular genetics and phylogenetic analysis, sometimes contradict traditional taxonomic classifications based on morphology (Viot and Wendel, 2023). These discrepancies necessitate a reevaluation of taxonomic frameworks to integrate both classical and molecular data for a more accurate classification. Figure 1 Evolution of the allopolyploid cotton genome (Adopted from Hu et al., 2019) Image caption: (a) Evolutionary analysis of the G. barbadense and G. hirsutumgenomes, showing the Ks distribution of orthologous genes, indicating that the divergence time of these species is between 0.4 and 0.6 million years ago. (b) Comparison of the codon substitution rate distribution between the two subgenomes of TM-1 and Hai7124 and their progenitors, revealing the accelerated evolution of the cotton genome. (c) Distribution of SNPs, indels, PAVs, inversions, and translocations in the TM-1 and Hai7124 genomes. This figure illustrates the genetic and structural variations in the cotton genome during evolution (Adapted from Hu et al., 2019) 5.4 Impact of hybridization events Hybridization events within the Gossypium genus have a profound impact on taxonomy. The occurrence of interspecific hybridizations, both intentional and unintentional, has led to the creation of new genetic combinations and the blurring of species boundaries. The dual domestication and subsequent hybridization of Gossypium barbadense and Gossypium hirsutum exemplify how hybridization can complicate taxonomic classification (Viot and Wendel, 2023). Additionally, the identification of introgression events from Gossypium
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