1 Introduction

Gossypium plants, as the fundamental pillar of the global textile industry, are highly favored for their fiber length, high strength, and good softness. These plants not only provide abundant economic resources for human society, but also offer a unique perspective for plant science research. With the rapid development of modern biotechnology, research on the genetic diversity and evolutionary history of cotton plants is becoming increasingly in-depth.

The genus Gossypium, commonly known as cotton, comprises approximately 50 species distributed across tropical and subtropical regions worldwide, excluding Europe (Viot and Wendel, 2023). These species are categorized into diploid and allotetraploid groups, with the latter including the economically significant Gossypium hirsutum and Gossypium barbadense (Wang et al., 2018; Hu et al., 2019). The evolutionary history of Gossypium is marked by complex events such as polyploidization, hybridization, and domestication, which have contributed to the genetic diversity observed within the genus (Huang et al., 2020; Viot and Wendel, 2023). The diploid species, particularly those in the D-genome group, are of significant interest due to their role as one of the parental genomes of cultivated tetraploid cottons (Small and Wendel, 2000).

Phylogenetic analysis is a crucial tool in plant science for understanding the evolutionary relationships and genetic diversity among species. In the context of Gossypium, phylogenetic studies have provided insights into the rapid diversification and radiation of cotton genome groups (Cronn et al., 2002; Wu et al., 2018). These analyses utilize various molecular markers, including nuclear and chloroplast DNA sequences, to resolve the branching order and evolutionary history of cotton species (Wu et al., 2018; Cronn et al., 2002). The integration of phylogenetic data with genomic resources has also facilitated the identification of structural variations and gene families responsible for key traits such as fiber quality and stress resilience (Wang et al., 2018; Hu et al., 2019). Moreover, phylogenetic analysis aids in the conservation and utilization of genetic resources, enabling the development of improved cotton varieties through breeding programs (Kushanov et al., 2022).

This study provides a comprehensive overview of the phylogenetic relationships among Gossypium species. It summarizes the current understanding of the evolutionary history and genetic relationships within the genus Gossypium, drawing on recent phylogenetic studies and genomic analyses. The study highlights the methodologies and molecular markers used in phylogenetic studies of Gossypium, emphasizing the importance of using multiple, independent data sets for accurate resolution of phylogenetic relationships. Additionally, it discusses the implications of phylogenetic findings for cotton breeding and genetic improvement, particularly in terms of fiber quality, disease resistance, and environmental adaptability. By synthesizing information from various studies, this study aims to enhance the understanding of genetic diversity and evolutionary dynamics of Gossypium species, ultimately promoting the advancement of cotton research and breeding efforts.

2 Overview of Gossypium Genus

The genus Gossypium, commonly known as cotton, is of significant economic importance due to its fiber, which is a primary raw material for the textile industry. This genus is also a model system for studying plant evolution, polyploidy, and genome organization.

2.1 Taxonomy and classification

The genus Gossypium, commonly known as cotton, belongs to the Malvaceae family and comprises approximately 50 species distributed globally in tropical and subtropical regions. Taxonomically, Gossypium is divided into eight diploid genome groups (A, B, C, D, E, F, G, and K) and one allotetraploid group (AD) (Chen et al., 2016). Gossypium is classified into eight diploid genome groups (A-G and K) and one allotetraploid group (AD) (Chen et al., 2017; Wu et al., 2018; Huang et al., 2020). The diploid species are distributed across three major clades corresponding to their geographic origins: Africa (A-, E-, and F-genomes), the Americas (D-genome), and Australia (C-genomes and G-genomes). The allotetraploid group (AD) originated from hybridization events between A-genome and D-genome species.

Cotton plants are known for their unique morphological characteristics, such as annual or perennial herbaceous habits, as well as leaf palmate division. Based on the characteristic of chromosome number x=13, cotton species are further classified, reflecting their close genetic relationship.The classification is based on morphological characteristics, geographical distribution, and molecular data, which have helped to clarify the relationships among the species (Cronn et al., 2002). Recent molecular phylogenetic studies have utilized various markers, including nuclear and chloroplast DNA sequences, to provide a more resolved classification of the genus (Grover et al., 2015).

2.2 Evolutionary history

The evolutionary history of Gossypium is marked by events of polyploidy and rapid diversification. The genus originated approximately 5-10 million years ago, with polyploidization events leading to the formation of allotetraploid species around 1-2 million years ago (Senchina et al., 2003). The genus is believed to have originated in Africa or Australia, with subsequent long-distance dispersal events leading to the colonization of the Americas. The formation of allotetraploid cottons (AD-genome) is a significant evolutionary event, resulting from hybridization between diploid species from different continents. Molecular studies have shown that the A-genomes and D-genomes evolved independently, with no direct ancestor-progeny relationship (Huang et al., 2020). The divergence of Gossypium from its nearest relatives in the genera Kokia and Gossypioides occurred approximately 17% of the time since their separation (Cronn et al., 2002).

Huang et al. (2020) studied the evolutionary history of allotetraploid cotton (AD-genome). The study emphasizes the complexity of cotton genome evolution, underscoring the critical genetic variations and evolutionary events that shaped modern cotton species.

2.3 Distribution and Diversity

Gossypium species are distributed across tropical and subtropical regions worldwide. The genus exhibits significant diversity, with species adapted to a wide range of ecological niches. The diploid species are primarily found in Africa, the Americas, and Australia, while the allotetraploid species are predominantly found in the New World. The genetic diversity within the genus is reflected in the variation in chloroplast genome structure, gene order, and GC content among differen species (Figure 1) (Wu et al., 2018). The genus has also undergone extensive introgression and hybridization, contributing to its genetic diversity.

Wu et al. (2018) studied the distribution and types of repeated sequences in different Gossypium (cotton) species, reflecting their genetic diversity. Figure 2A shows the number of different types of repeated sequences in each species, revealing differences in the structure of chloroplast genomes. Figure 2B summarizes the distribution of these repeated sequences in different genome groups, indicating that the AD genome of allotetraploid cotton exhibits higher complexity and diversity. Figures 2C and 2D illustrate the proportion of repeated sequence lengths and their distribution in functional regions of the genome, further explaining the diversity in gene order and structure. This study highlights the important role of repeated sequences in the evolution and diversity of cotton genomes, providing significant insights into the evolutionary history and genetic diversity of Gossypium species and offering a crucial basis for understanding the evolutionary history and genomic characteristics of cotton.

3 Methodologies in Phylogenetic Analysis

3.1 Molecular markers used in Gossypium studies

Chloroplast DNA (cpDNA) has been extensively used in phylogenetic studies of Gossypium due to its maternal inheritance and relatively conserved nature. Studies have utilized various cpDNA regions to resolve phylogenetic relationships among Gossypium species. For instance, the analysis of 13 Gossypium chloroplast genomes revealed high sequence similarity and provided insights into the evolutionary mechanisms of allotetraploids (Xu et al., 2012). Additionally, the use of noncoding cpDNA regions has been shown to offer phylogenetic information at low taxonomic levels, although the resolution can be limited (Shaw et al., 2005). The phylogenetic informativeness of different cpDNA markers has also been evaluated, with certain regions like the rpl32-ndhF intergenic spacer and trnL-rpl32 IGS being identified as highly informative (Mendoza et al., 2013).

Nuclear DNA markers, particularly single-copy nuclear genes, have proven valuable in resolving phylogenetic relationships within Gossypium. These markers offer higher variability compared to cpDNA and can help detect reticulation events. For example, the use of 11 single-copy nuclear loci and nuclear ribosomal DNA has provided significant insights into the rapid radiation of cotton genome groups (Cronn et al., 2002). The development of phylogenetic markers from single-copy nuclear genes has also been demonstrated in other plant families, highlighting their utility in species-level analyses (Curto et al., 2012).

Mitochondrial DNA (mtDNA) is less commonly used in plant phylogenetics due to its lower rate of evolution and potential for recombination. However, it can still provide valuable information in certain contexts. In Gossypium, mtDNA has been used in conjunction with cpDNA and nuclear DNA to provide a more comprehensive understanding of phylogenetic relationships. For example, targeted enrichment of intron-containing sequence markers has been employed to resolve recent radiations, with organellar phylogenies being well-supported and sometimes conflicting with nuclear signals (Folk et al., 2015).

3.2 Techniques and tools for phylogenetic analysis

Sequence alignment is a critical step in phylogenetic analysis, ensuring that homologous sequences are compared accurately. Various tools and algorithms are available for sequence alignment, including ClustalW, MUSCLE, and MAFFT. These tools help align sequences from different molecular markers, such as cpDNA, nuclear DNA, and mtDNA, facilitating the construction of phylogenetic trees. Accurate alignment is essential for subsequent analyses, as misalignments can lead to incorrect phylogenetic inferences.

Phylogenetic tree construction involves the use of various methods to infer evolutionary relationships among species. Common methods include Maximum Likelihood (ML), Bayesian Inference (BI), and Parsimony Analysis. For example, ML analysis of nuclear synonymous sites has been used to study the rapid radiation of Gossypium genome groups (Cronn et al., 2002). Parsimony analysis, including character-state weighting approaches, has also been employed to model the relative probabilities of restriction site losses versus gains in cpDNA studies. These methods help generate robust phylogenetic hypotheses and provide insights into the evolutionary history of Gossypium species.

Several software programs and algorithms are available for phylogenetic analysis, each with its strengths and limitations. Popular software includes MEGA, BEAST, MrBayes, and PAUP*. These programs offer various functionalities, such as sequence alignment, model selection, tree construction, and hypothesis testing. For instance, the phylogenetic informativeness method has been applied to chloroplast markers to prioritize loci for phylogenetic studies. Additionally, the use of coalescent and concatenated phylogenetic analyses has demonstrated support for major relationships in recent radiations (Folk et al., 2015). The choice of software and algorithms depends on the specific requirements of the study and the nature of the data being analyzed.

By employing a combination of molecular markers, alignment techniques, tree construction methods, and specialized software, researchers can achieve a comprehensive understanding of the phylogenetic relationships within Gossypium. This multi-faceted approach ensures robust and accurate phylogenetic inferences, contributing to our knowledge of cotton evolution and genetic diversity.

4 Findings from Phylogenetic Studies

4.1 Genetic relationships among Gossypium species

Phylogenetic studies have provided significant insights into the genetic relationships among Gossypium species. The analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes revealed a high degree of conservation, with sequence variations that help delineate the relationships between allotetraploid species and their diploid progenitors (Xu et al., 2012). Additionally, the genome sequence of Gossypium herbaceum and updates to the genomes of Gossypium arboreum and Gossypium hirsutum have shown that all existing A-genomes may have originated from a common ancestor, providing a clearer picture of the phylogenetic relationships within the genus (Huang et al., 2018). Furthermore, the phylogenetic analysis of ribosomal DNA sequences from Gossypium gossypioides has uncovered ancient intergenomic introgression events, suggesting complex genetic relationships and hybridization histories among species.

4.2 Divergence and speciation events

Divergence and speciation events in Gossypium have been shaped by both polyploidization and structural genomic changes. The formation of allotetraploid cotton species, such as Gossypium hirsutum and Gossypium barbadense, has been a key driver of speciation, with these species evolving to produce higher fiber yields and better environmental resilience (Hu et al., 2018). Comparative genomics analyses have identified extensive structural variations, including large chromosomal inversions, that likely occurred after polyploidization and contributed to the speciation of these cotton species (Wang et al., 2018). Additionally, the genome sequence data suggest that the speciation of A1 and A2 genomes occurred independently, with significant structural variations in genic regions influencing the evolution and speciation of these genomes (Huang et al., 2018).

4.3 Hybridization and polyploidy

Hybridization and polyploidy have played crucial roles in the evolution and diversification of Gossypium species. The phylogenetic analysis of nuclear and plastid DNA sequences has supported the occurrence of polyploid chromosome number changes and reticulate evolution, indicating that hybridization events have been important in the diversification of the genus (Blöch et al., 2009). The study of ribosomal DNA sequences from Gossypium gossypioides has provided evidence of ancient hybridization events and intergenomic introgression, highlighting the role of hybridization in shaping the genetic makeup of Gossypium species (Hu et al., 2018). Moreover, the reference genome sequences of Gossypium hirsutum and Gossypium barbadense have revealed species-specific alterations in gene expression and structural variations, further underscoring the impact of hybridization and polyploidy on the evolution of these cotton species (Hu et al., 2018).

Hu et al. (2018) conducted an evolutionary analysis of allotetraploid cotton genomes, focusing particularly on the impact of hybridization and polyploidization on the evolution of cotton species. Figure (a) shows the distribution of synonymous substitution rates (Ks), while Figure (b) compares the substitution rates between the two subgenomes (TM-1 and Hai7124) and their progenitor species, revealing significant differences. Figure (c) displays the distribution and differences in SNPs, indels, PAVs, inversions, and translocations between the TM-1 and Hai7124 genomes. These data indicate that through hybridization and polyploidization, cotton species have accumulated substantial genetic variation, significantly affecting genome structure and evolutionary pathways. The study suggests that hybridization and polyploidization are crucial mechanisms driving the diversity and adaptability of cotton species.

5 Implications of Phylogenetic Insights

5.1 Understanding genetic diversity

Phylogenetic analysis of Gossypium species has significantly enhanced our understanding of genetic diversity within the genus. Studies have revealed substantial variation in DNA content among diploid species, with more than a two-fold difference observed. This genetic diversity is further underscored by the identification of numerous polymorphic bands through RAPD analysis, which demonstrated a wide genetic base among species (Khan et al., 2000). Additionally, the discovery of large-scale repeat sequences in chloroplast genomes, particularly in F-genome species, suggests that these repeats may play a role in enriching genetic information and maintaining genome stability (Wu et al., 2018). These insights into genetic diversity are crucial for understanding the evolutionary history and adaptive potential of Gossypium species.

5.2 Conservation and breeding strategies

The phylogenetic relationships elucidated through various molecular analyses have important implications for conservation and breeding strategies. For instance, the identification of divergence hotspot regions in chloroplast genomes can serve as valuable molecular markers for future population genetics and phylogenetic studies (Wu et al., 2018). Moreover, the phylogenetic clustering of species into distinct clades based on genome types (e.g., A-, D-, and F-genomes) provides a framework for selecting genetically diverse parent lines for breeding programs. Understanding the genetic relationships among species can also aid in the conservation of genetic resources by identifying unique and endangered lineages that require protection (Huang et al., 2020).

5.3 Evolutionary and ecological insights

Phylogenetic studies have provided profound insights into the evolutionary and ecological dynamics of Gossypium species. The rapid diversification of the genus, as revealed by nuclear and chloroplast gene analyses, suggests a history of rapid radiation following the formation of the genus (Cronn et al., 2002). This rapid radiation is further supported by the incongruence observed between chloroplast and nuclear phylogenies, which may be attributed to hybridization events and limited character evolution in cpDNA (Cronn et al., 2002). Additionally, the discovery of ancient hybridization and introgression events, such as those involving G. gossypioides, highlights the complex evolutionary history of the genus and the role of intergenomic interactions in shaping current species distributions. These evolutionary insights are essential for understanding the adaptive strategies and ecological niches occupied by different Gossypium species.

5.4 Practical applications in cotton improvement

The phylogenetic insights gained from these studies have practical applications in cotton improvement. For example, the assembly of the Gossypium herbaceum genome and updates to the Gossypium arboreum and Gossypium hirsutum genomes have provided valuable genomic resources for cotton genetic improvement (Wang et al., 2018). These genomic resources can be used to identify genes associated with desirable traits, such as fiber quality and disease resistance, and to develop molecular markers for marker-assisted selection in breeding programs. Furthermore, the understanding of phylogenetic relationships among species can guide the introgression of beneficial traits from wild relatives into cultivated varieties, thereby enhancing the genetic diversity and resilience of cotton crops (Grover et al., 2015).

6 Challenges and Future Directions

6.1 Limitations in current studies

Current phylogenetic studies on Gossypium species face several limitations. One significant challenge is the low phylogenetic resolution within recently diverged taxa due to a paucity of informative characters. For instance, noncoding plastome regions often provide insufficient resolution, as seen in the study of tetraploid cottons where only four informative nucleotide substitutions were found across over 7 kb of sequence data. Additionally, the reliance on single-gene or limited multi-gene analyses can lead to weak support for certain phylogenetic branches, as observed in the reevaluation of allopolyploid cotton species (Grover et al., 2015). Another limitation is the incongruence between different data types, such as nuclear and plastid DNA, which can complicate phylogenetic interpretations. Furthermore, the presence of cryptic intergenomic introgression events, as revealed by unusual ribosomal DNA sequences, adds another layer of complexity to understanding the evolutionary history of Gossypium species.

6.2 Technological advancements

Advancements in genomic technologies offer promising avenues to overcome these limitations. High-throughput sequencing technologies, such as whole genome resequencing, provide comprehensive data that can enhance phylogenetic resolution. For example, genome sequencing of Gossypium herbaceum and improvements in the genomes of Gossypium arboreum and Gossypium hirsutum have provided valuable insights into the phylogenetic relationships and origin history of cotton A-genomes (Huang et al., 2020). Additionally, targeted sequence capture and the use of multiple loci in conjunction with both concatenated and Bayesian concordance analyses have shown to provide robust support for phylogenetic clades (Grover et al., 2015). The application of fluorescent in situ hybridization (FISH) to investigate chromosomal locations of rDNA also offers a powerful tool for understanding evolutionary relationships and chromosomal rearrangements in Gossypium species.

6.3 Future research opportunities

Future research should focus on integrating multiple data types and employing comprehensive genomic approaches to resolve phylogenetic relationships more accurately. One promising direction is the use of phylogenomic methods to study molecular evolutionary processes and phylogeny, as demonstrated in the analysis of New World diploid cottons (Grover et al., 2018). Additionally, exploring the differential amplification of transposable elements and their impact on genome size variation can provide insights into the evolutionary dynamics of Gossypium genomes (Hawkins et al., 2006). Another area of interest is the investigation of interspecific introgression events and their role in shaping the genetic diversity of Gossypium species. Finally, expanding the use of advanced sequencing technologies and bioinformatics tools will enable more detailed and accurate phylogenetic analyses, ultimately contributing to the genetic improvement of cotton species (Grover et al., 2015; Khan et al., 2000; Huang et al., 2020).

7 Concluding Remarks

The systematic review of phylogenetic analysis in Gossypium species has provided several key insights into the genetic relationships and evolutionary history of this economically significant genus. The assembly and improvement of Gossypium genomes have clarified the origins and evolutionary pathways of A-genomes, revealing that all existing A-genomes may have originated from a common ancestor, A0, which is more closely related to G. herbaceum (A1) than G. arboreum (A2). Comparative chloroplast genomics have highlighted the role of repeat sequence variations in maintaining genome stability and provided new molecular markers for future phylogenetic studies. Additionally, the discovery of ancient intergenomic introgression events has shed light on the complex evolutionary history of Gossypium species. The use of both plastome and nuclear sequences has demonstrated the importance of selecting appropriate genetic markers for resolving phylogenetic relationships in recently diverged taxa.

Phylogenetic analysis plays a crucial role in Gossypium research by providing a framework for understanding the genetic relationships and evolutionary history of cotton species. It has enabled researchers to trace the origins of allopolyploid cottons and their rapid diversification in response to environmental changes. The use of various genetic markers, including chloroplast DNA, nuclear genes, and transposable elements, has allowed for a comprehensive analysis of genome evolution and the identification of lineage-specific amplification events. These insights are essential for cotton breeding programs, as they inform the selection of parent species for hybridization and the development of improved cotton varieties with desirable traits.

In conclusion, the phylogenetic analysis of Gossypium species has provided valuable insights into the genetic relationships and evolutionary history of this important genus. Future research should focus on expanding the genomic resources available for Gossypium species, including the sequencing of additional diploid and polyploid genomes. This will enable a more detailed understanding of the genetic diversity within the genus and facilitate the identification of key genes involved in fiber development and other important traits. Additionally, the integration of phylogenetic data with other types of genomic and phenotypic data will provide a more comprehensive understanding of the evolutionary processes shaping Gossypium species. Researchers should also consider the potential impact of ancient hybridization events and intergenomic introgression on the genetic makeup of modern cotton species, as these events may have important implications for cotton breeding and genetic improvement.

Acknowledgments

Sincere gratitude to the peer reviewers for their invaluable feedback on the preliminary version of this manuscript. Their insightful comments and constructive criticism have significantly contributed to enhancing the quality and clarity of this article.

Conflict of Interest Disclosure

The authors affirm 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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