Cotton Genomics and Genetics 2024, Vol.15, No.2, 81-92 http://cropscipublisher.com/index.php/cgg 83 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 hirsutumand 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 Gossypiumherbaceum and improved the existing genomes of Gossypium arboreumand 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 arboreumhave 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 Gossypiumspecies 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 Gossypiumspecies, 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 Gossypiumgenome 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
RkJQdWJsaXNoZXIy MjQ4ODYzNQ==