Cotton Genomics and Genetics 2024, Vol.15, No.2, 81-92 http://cropscipublisher.com/index.php/cgg 84 instance, the use of chloroplast genome sequences has provided insights into the phylogenetic relationships and repeat sequence variations among Gossypium species, aiding in more accurate species delineation (Wu et al., 2018). Additionally, the development of synthetic allotetraploids through distant hybridization has expanded the genetic resources available for species identification and breeding (Yin et al., 2020). 4.3 Subgenus and section level classifications At the subgenus and section levels, Gossypium species are classified based on their genomic composition and evolutionary history. Comparative genomics and whole-genome sequencing have revealed significant structural variations and gene family expansions that contribute to the speciation and evolutionary history of Gossypium(Hu et al., 2019; Yang et al., 2020). Hu et al. (2019) studied the whole genome sequences of two cultivated species, Gossypium barbadense and Gossypium hirsutum. The study revealed species-specific changes in gene expression, structural variations, and gene family expansions through high-quality de novo assembly, which are key factors in species differentiation and evolution (Figure 1). Studies have identified distinct genetic clades within the genus, with the D-genome species forming a strong monophyletic clade, while C, G, and K-genome species exhibit more complex relationships due to recent radiation and hybridization events (Wu et al., 2018). 4.4 Hybridization and polyploidy inGossypium Hybridization and polyploidy are central to the evolution and diversification of Gossypium. The genus includes both diploid and allotetraploid species, with the latter resulting from hybridization events between A-genome and D-genome species (Hu et al., 2019; Anwar et al., 2022). Polyploidization has led to the formation of new species with unique genetic and phenotypic traits, contributing to the adaptability and economic importance of cotton (Mandák et al., 2018; Hörandl, 2022). Modern genomic tools have facilitated the identification of quantitative trait loci (QTLs) associated with desirable traits, such as fiber quality, in hybrid and polyploid cotton species (Wang et al., 2019; Anwar et al., 2022). 5 Challenges and Controversies inGossypiumTaxonomy 5.1 Issues with morphological variability Morphological variability within the Gossypiumgenus presents significant challenges in taxonomic classification. The extensive diversity in physical traits such as plant architecture, leaf shape, and fiber characteristics complicates the identification and classification of species. For instance, the study of Gossypiumpopulations in Amazonian Native Communities revealed substantial morphological diversity, which may result from spontaneous crosses and environmental adaptations, making it difficult to delineate clear taxonomic boundaries (Morales-Aranibar et al., 2023). Additionally, the variability in morphological traits can be influenced by both genetic and environmental factors, further complicating taxonomic efforts (Kushanov et al., 2022). 5.2 Genetic divergence and convergence Genetic divergence and convergence within Gossypiumspecies add another layer of complexity to taxonomy. The introgression from Gossypium hirsutum to Gossypium barbadense has significantly reorganized the genomic architecture of the latter, leading to increased genetic diversity and divergence (Wang et al., 2022). This genetic mixing can obscure species boundaries and create challenges in distinguishing between species based solely on genetic data. Moreover, the independent evolution of A-genomes in Gossypium herbaceum and Gossypium arboreum, despite their common ancestry, highlights the complexity of genetic divergence within the genus (Huang et al., 2020). The study shows that there is no ancestor-descendant relationship between the A1 and A2 genomes, and that the two A-genomes evolved independently (Figure 2). The research also found that multiple long terminal repeat (LTR) bursts contributed significantly to the size expansion, species formation, and evolution of the A-genomes. These findings clarify the controversy over the origin of the A-genomes, provide insights into the phylogenetic relationships and origin history of the cotton A-genomes, and offer valuable genetic resources for cotton improvement (Huang et al., 2020). 5.3 Discrepancies between classical and molecular data Discrepancies between classical taxonomic methods and modern molecular data often lead to controversies in Gossypiumtaxonomy. Classical methods, which rely heavily on morphological traits, may not always align with
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