1 Introduction

The genus Gossypium, commonly known as cotton, belongs to the Malvaceae family and comprises approximately 50 species distributed across tropical and subtropical regions worldwide, excluding Europe (Viot and Wendel, 2023). Gossypium species are notable for their economic importance, particularly in the production of natural fibers. The genus includes both diploid and allotetraploid species, with the latter resulting from polyploidization events that have significantly influenced their evolutionary trajectory (Paterson et al., 2012; Hu et al., 2019). The evolutionary history of Gossypium is marked by rapid diversification and complex phylogenetic relationships, which have been elucidated through extensive molecular and genetic studies (Cronn et al., 2002; Wu et al., 2018).

Gossypium species are of immense agricultural and economic significance due to their role in the global textile industry. Gossypium hirsutum and Gossypium barbadense are the two primary species cultivated for their superior fiber qualities, with G. hirsutum being the most widely grown due to its high yield and adaptability, and G. barbadense valued for its superior fiber properties (Yuan et al., 2015; Wang et al., 2018; Hu et al., 2019). Beyond their economic value, Gossypium species also serve as a model for studying polyploidy and plant domestication, providing insights into the genetic and molecular mechanisms underlying fiber development and environmental resilience (Zhang et al., 2018; Yang et al., 2020). Additionally, the genus has ethnobotanical relevance, with various species used in traditional medicine for their antimicrobial properties (De Lima et al., 2021).

This study aims to provide a comprehensive overview of the classification of the Gossypium genus, tracing its historical perspective and highlighting modern advancements. By integrating data from phylogenetic studies, genomic analyses, and ethnobotanical research, the study elucidates the evolutionary relationships within the genus and the genetic basis of its domestication and diversification. This study will also explore the impact of recent genomic discoveries on cotton breeding and improvement, emphasizing the potential to enhance fiber quality and environmental adaptability. Through this integrated analysis, the study aspires to offer a detailed understanding of the complexity and evolutionary dynamics of Gossypium classification, contributing to the broad knowledge of plant evolution and agricultural biotechnology.

2 Historical Perspectives on Gossypium Classification

2.1 Early taxonomic efforts

The initial taxonomic efforts to classify the genus Gossypium were spearheaded by Todaro in the mid-19th century, with significant contributions in 1863 and 1877. These early studies provide a theoretical foundation for understanding the genus, which is economically important due to its cotton fiber production (Fryxell, 1969). Following Todaro, Watt's major treatise in 1907 further advanced the classification, providing a more detailed understanding of the genus (Fryxell, 1969).

2.2 Classical morphological studies

Classical morphological studies played a crucial role in the taxonomic classification of Gossypium. Botanists began to employ more rigorous morphological studies, examining various plant parts such as leaves, flowers, seeds, and fibers in detail. This period saw the publication of several monographs and floras that described and categorized Gossypium species based on their morphological traits. Notable contributions came from botanists such as Alphonse de Candolle and Asa Gray, who systematically documented the diversity within the genus (Hoquet, 2014; Haufler, 2015). These morphological studies provided a more structured framework for distinguishing between species, despite the limitations imposed by the lack of genetic and molecular tools. Furthermore, researchers like Zaitzev (1928) and Mauer (1930) made significant conceptual advances by focusing on the morphological characteristics of the species (Fryxell, 1969). These studies were instrumental in identifying and categorizing various species within the genus based on observable traits.

2.3 Contributions of Linnaean taxonomy

The advent of Linnaean taxonomy in the 18th century marked a pivotal moment in the classification of Gossypium. Carl Linnaeus, the father of modern taxonomy, introduced a binomial nomenclature system that brought uniformity and consistency to species classification (Zhang and Shea, 2007). Linnaeus himself classified several Gossypium species, providing a theoretical foundation for subsequent taxonomic work. The Linnaean system emphasized the importance of hierarchical classification and species naming conventions, which greatly influenced botanical taxonomy. Linnaeus’s contributions were instrumental in organizing the existing knowledge of Gossypium species and facilitating further taxonomic research.

The Linnaean system of taxonomy, which classifies organisms based on a hierarchical structure, was applied to Gossypium by several researchers. Hutchinson's treatment in 1947 is perhaps the most widely accepted modern classification, despite some nomenclatural inadequacies (Fryxell, 1969). Prokhanov (1947) and Roberty (1942, 1946, 1950) also contributed to the Linnaean taxonomy of Gossypium, although their classifications were often considered chaotic and less useful (Fryxell, 1969).

2.4 Evolution of Gossypium classification over time

The classification of Gossypium has evolved significantly over time, incorporating new data from various scientific disciplines. Modern studies have integrated molecular genetics, biogeography, and phylogenetic analysis to provide a more comprehensive understanding of the genus (Huang et al., 2020; Viot and Wendel, 2023). For instance, the evolutionary history of Gossypium has been elucidated through the analysis of nuclear and chloroplast genes, revealing rapid diversification and complex hybridization events (Cronn et al., 2002). Additionally, the genome sequencing of Gossypium species has provided insights into the phylogenetic relationships and evolutionary history of cotton genomes (Hu et al., 2019; Huang et al., 2020).

3 Modern Advances in Gossypium Taxonomy

3.1 Molecular phylogenetics

Molecular phylogenetics has significantly advanced our understanding of the evolutionary relationships within the Gossypium genus. By employing phylogenomic methods, researchers have been able to reassess the phylogenetic history of Gossypium, providing a temporal framework for its diversification. For instance, whole genome resequencing data has revealed that the New World diploid cottons likely originated following transoceanic dispersal from Africa about 6.6 million years ago, with most biodiversity evolving during the mid-Pleistocene (Grover et al., 2019). Additionally, the evolutionary history of Gossypium has been clarified through the integration of data from molecular genetics and phylogenetic analysis, uncovering multiple previously cryptic interspecific hybridizations (Viot and Wendel, 2023).

3.2 Genomic sequencing technologies

The advent of advanced genomic sequencing technologies has revolutionized the study of Gossypium. High-quality genome sequences of various Gossypium species have been generated using techniques such as single-molecule real-time sequencing, BioNano optical mapping, and high-throughput chromosome conformation capture. These technologies have provided reference-grade genome assemblies for species like Gossypium hirsutum and Gossypium barbadense, which are crucial for understanding cotton evolution and improving fiber quality (Wang et al., 2019). Huang et al. (2020) assembled the genome of Gossypium herbaceum and improved the existing genomes of Gossypium arboreum and Gossypium hirsutum, providing insights into the phylogenetic relationships and origin history of the cotton A-genomes.

3.3 Comparative genomics

Comparative genomics has played a pivotal role in elucidating the structural variations and evolutionary processes within Gossypium. For example, comparative analyses of the genomes of Gossypium raimondii and Gossypium arboreum have identified genome-specific repetitive elements that contribute to genome variation between the A and D genomes (Lu et al., 2020). Additionally, the comparison of genome sequences of Gossypioides kirkii with those of Gossypium species has revealed structural rearrangements such as chromosome fusions and inversions, which are essential for understanding the evolutionary dynamics of chromosome number variation in plants (Udall et al., 2019).

3.4 Role of bioinformatics in modern taxonomy

Bioinformatics has become an indispensable tool in modern taxonomy, enabling the analysis and interpretation of large-scale genomic data. The integration of bioinformatics techniques has facilitated the identification of quantitative trait loci associated with superior fiber quality in Gossypium species, thereby accelerating breeding programs (Wang et al., 2019). Moreover, the use of bioinformatics in the study of genome-specific repetitive elements has promoted research on Gossypium genome evolution and subgenome identification (Lu et al., 2020). The inclusion of novel descriptors such as associated microorganisms and mitochondrial genomes in taxonomic studies has also provided a deeper understanding of the evolutionary and ecological dimensions of organisms (Serra et al., 2020).

Modern advances in molecular phylogenetics, genomic sequencing technologies, comparative genomics, and bioinformatics have significantly enhanced our understanding of Gossypium taxonomy, providing valuable insights into the evolutionary history and genetic improvement of this economically important genus.

4 Current Taxonomic Classification of Gossypium

4.1 Overview of current classification systems

The genus Gossypium, commonly known as cotton, comprises approximately 50 species distributed across tropical and subtropical regions worldwide, excluding Europe (Viot and Wendel, 2023). The classification of Gossypium has evolved significantly with advancements in molecular genetics, cytogenetics, and phylogenetic analysis. Modern classification systems integrate these diverse data sources to provide a comprehensive understanding of species relationships and diversification within the genus (Wang et al., 2018; Wang et al., 2019). The genus is divided into several genome groups, including one allotetraploid group (AD) and eight diploid genome groups (A-G and K) (Wu et al., 2018).

4.2 Species delineation and identification

Species delineation within Gossypium has been historically challenging due to the complexity of hybridization and polyploidization events. Traditional morphological methods have been supplemented with molecular markers and genomic tools to improve species identification and classification (Yin et al., 2020; Hörandl, 2022) For 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 in Gossypium

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 in Gossypium Taxonomy

5.1 Issues with morphological variability

Morphological variability within the Gossypium genus 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 Gossypium populations 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 Gossypium species 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 Gossypium taxonomy. Classical methods, which rely heavily on morphological traits, may not always align with molecular phylogenetic analyses. For example, the evolutionary history and domestication of Gossypium species, 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.

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 hirsutum to Gossypium barbadense underscores the role of hybridization in shaping the genetic landscape of the genus (Wang et al., 2022).

5.5 Evolutionary dynamics and genome variation

The evolutionary dynamics and genome variation within Gossypium species pose significant challenges to taxonomy. The activity of genome-specific repetitive sequences, such as the ICRd motif in the D genome, contributes to genome variation and complicates the understanding of evolutionary relationships (Lu et al., 2020). The structural variations and gene expression changes observed in allotetraploid cotton species highlight the ongoing evolutionary processes that influence genome architecture and species differentiation (Hu et al., 2019). These dynamic evolutionary changes necessitate continuous updates to taxonomic classifications to reflect the current understanding of Gossypium genomics.

6 Applications of Gossypium Taxonomy in Breeding and Conservation

6.1 Implications for cotton breeding programs

The taxonomic classification of Gossypium has profound implications for cotton breeding programs. Understanding the genetic diversity and evolutionary history of Gossypium species allows breeders to identify and utilize favorable traits from wild and domesticated species. For instance, the reference genome sequences of Gossypium hirsutum and Gossypium barbadense have facilitated the identification of quantitative trait loci (QTLs) associated with superior fiber quality, which can be introgressed into breeding lines to improve cotton varieties (Hu et al., 2019; Wang et al., 2019). Additionally, the genetic analysis of mutagenesis in wild cotton species has identified candidate genes related to flowering traits, which can be used in marker-assisted selection to develop early-flowering and high-yielding cotton varieties (Kushanov et al., 2022).

6.2 Conservation strategies for wild Gossypium species

Conservation of wild Gossypium species is crucial for maintaining genetic diversity, which is essential for the long-term sustainability of cotton breeding programs. The genetic diversity of Gossypium populations in Amazonian native communities highlights the importance of preserving these genetic resources (Morales-Aranibar et al., 2023). Conservation strategies should focus on protecting natural habitats and promoting in situ conservation of wild species. Additionally, ex situ conservation methods, such as seed banks and botanical gardens, can be employed to safeguard genetic material for future use in breeding programs (Peng et al., 2022; Morales-Aranibar et al., 2023).

6.3 Utilization of genetic diversity

The genetic diversity within the Gossypium genus provides a valuable resource for improving cotton crops. Comparative genomics and phylogenetic studies have revealed extensive structural variations and gene family expansions that contribute to the adaptation and resilience of different Gossypium species (Wu et al., 2018; Hu et al., 2019). By leveraging this genetic diversity, breeders can introduce traits such as disease resistance, drought tolerance, and improved fiber quality into cultivated cotton varieties. The identification of divergence hotspot regions and site-specific selection in chloroplast genomes further aids in understanding the evolutionary relationships and potential for genetic improvement (Wu et al., 2018).

6.4 Case studies in breeding and conservation

Several case studies illustrate the successful application of Gossypium taxonomy in breeding and conservation efforts. For example, the introgression of favorable chromosome segments from Gossypium barbadense into Gossypium hirsutum has led to the development of cotton lines with enhanced fiber quality (Wang et al., 2019). Wang et al. (2019) conducted a detailed analysis of the reference genome sequences of two cultivated cotton species, Gossypium hirsutum and Gossypium barbadense. The study employed single-molecule real-time sequencing, optical mapping, and high-throughput chromosome conformation capture techniques to construct high-quality genome assemblies for both species. Comparative genomic analysis revealed multiple structural variations. Additionally, a backcross population incorporating the superior fiber traits of G. barbadense was constructed, leading to the identification of 13 quantitative trait loci (QTLs) related to fiber quality (Figure 3). These resources will enhance research on cotton evolution and functional genomics, providing a reference for future fiber improvement breeding programs.

Another case study involves the genetic analysis of Gossypium herbaceum and Gossypium arboreum, which has provided insights into their independent domestication and interspecific gene flow, informing breeding strategies for these diploid species (Huang et al., 2020; Grover et al., 2022). These examples demonstrate the practical benefits of integrating taxonomic knowledge into breeding and conservation programs.

The taxonomic classification of Gossypium plays a critical role in advancing cotton breeding and conservation efforts. By understanding the genetic diversity and evolutionary history of Gossypium species, researchers and breeders can develop improved cotton varieties and implement effective conservation strategies to ensure the sustainability of this economically important crop.

7 Future Directions in Gossypium Taxonomic Research

7.1 Integration of multi-omics approaches

The integration of multi-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, holds significant promise for advancing the taxonomic classification of Gossypium. By leveraging these comprehensive datasets, researchers can gain deeper insights into the genetic and molecular underpinnings of species differentiation and evolutionary relationships. For instance, the assembly of high-quality reference genomes for Gossypium hirsutum and Gossypium barbadense has already provided valuable resources for comparative genomics and evolutionary studies (Wang et al., 2019). Additionally, the improved genome sequences of Gossypium herbaceum and Gossypium arboreum have shed light on the phylogenetic relationships and evolutionary history of cotton A-genomes (Huang et al., 2020). Future research should focus on integrating these multi-omics datasets to refine the taxonomic classification and uncover novel insights into the evolutionary dynamics of the Gossypium genus.

7.2 Advancements in computational methods

Advancements in computational methods, including machine learning and artificial intelligence, offer new opportunities for enhancing the accuracy and efficiency of taxonomic classification in Gossypium. These methods can be employed to analyze large-scale genomic and phenotypic datasets, identify patterns, and predict evolutionary relationships. For example, the use of high-throughput sequencing technologies and bioinformatics tools has enabled the construction of detailed phylogenetic trees and the identification of structural variations in cotton genomes (Wang et al., 2019). By incorporating advanced computational techniques, researchers can further refine these analyses and develop more robust taxonomic frameworks. Additionally, the application of computational methods to integrate and analyze multi-omics data will facilitate a more comprehensive understanding of the genetic and phenotypic diversity within the Gossypium genus.

7.3 Potential for CRISPR and genetic editing technologies

The advent of CRISPR and other genetic editing technologies has revolutionized the field of plant genetics and offers significant potential for advancing Gossypium taxonomic research. CRISPR/Cas9 and related systems have been successfully applied to create targeted gene mutations and study gene function in Gossypium species (Zhang et al., 2018; Qin et al., 2020; Li et al., 2021). For instance, the development of a CRISPR/Cas9 system for Gossypium hirsutum has enabled the generation of transgene-clean edited plants with enhanced disease resistance (Zhang et al., 2018). Similarly, the use of a modified CRISPR/Cas9 system for base editing in Gossypium hirsutum has demonstrated high specificity and accuracy for creating point mutations (Qin et al., 2020). Future research should explore the potential of these technologies to investigate the genetic basis of taxonomic traits, facilitate the creation of novel germplasm, and enhance our understanding of the evolutionary processes shaping the Gossypium genus.

7.4 Collaborative international research efforts

Collaborative international research efforts are essential for advancing Gossypium taxonomic research and addressing the complex challenges associated with the classification and conservation of cotton species. By fostering collaborations between researchers, institutions, and countries, it is possible to pool resources, share knowledge, and leverage diverse expertise. For example, the establishment of standardized cytogenetic and genomic nomenclature for Gossypium has facilitated comparative studies and breeding programs worldwide (Wang et al., 2018). Additionally, international collaborations have contributed to the assembly of high-quality reference genomes and the identification of genetic diversity in cotton populations (Wang et al., 2019; Morales-Aranibar et al., 2023). Future research should continue to promote collaborative efforts to enhance the taxonomic classification, conservation, and sustainable utilization of Gossypium species on a global scale.

8 Concluding Remarks

The taxonomic classification of the genus Gossypium has undergone significant advancements through historical and modern research. Early taxonomic investigations laid the groundwork for understanding the genus's diversity, which includes approximately 50 species distributed globally, except in Europe. Modern phylogenetic and genomic studies have provided deeper insights into the evolutionary history and domestication processes of key species such as Gossypium barbadense and Gossypium hirsutum. These studies have revealed the complex interplay of polyploidization, interspecific hybridization, and introgression events that have shaped the current genetic landscape of cotton. Additionally, the genetic diversity within native populations, particularly in regions like the Amazonian Native Communities, has been documented, highlighting the role of local cultivation practices in maintaining genetic variability.

These findings emphasize the importance of combining traditional taxonomic methods with modern genomic technologies to fully understand the evolutionary dynamics of the Gossypium genus. Future efforts should continue to focus on sequencing and annotating the genomes of more Gossypium species, providing a more comprehensive understanding of the genetic diversity and evolutionary history of the genus. Investigating the functional roles of specific genes and transposons in cotton adaptability and fiber quality is crucial for breeding programs aimed at improving crop resilience and productivity. Future research should also strive to preserve the genetic diversity in native populations, as these populations may harbor unique traits valuable for future breeding efforts. Additionally, further studies on the impact of polyploidy on gene expression and genome stability will enhance researchers' understanding of the success of polyploid species such as G. hirsutum and G. barbadense.

The taxonomic classification and evolutionary study of Gossypium have greatly benefited from the integration of historical perspectives and modern genomic advances. These efforts have not only clarified the complex evolutionary history of this economically important genus but also provided valuable resources for future research and breeding programs. By continuing to explore the genetic and functional diversity within Gossypium, researchers can develop more resilient and productive cotton varieties, ensuring the sustainability of this vital crop in the face of changing environmental conditions.

Acknowledgments

The CropSci Publisher appreciates the feedback from two anonymous peer reviewers on the manuscript of this study, whose careful evaluation and constructive suggestions have contributed to the improvement of the manuscript.

Conflict of Interest Disclosure

The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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