Bioscience Evidence 2025, Vol.15, No.5, 219-227 http://bioscipublisher.com/index.php/be 220 and G. raimondii) is relatively simple. Allotetraploid cotton (such as G. hirsutum, G. barbadense) is formed by the combination of two subgenomes, A and D, with doubled chromosome numbers and a more complex genome (Wang et al., 2018; Hu et al., 2019; Huang et al., 2020) (Figure 1). Tetraploid cotton was formed approximately 1 to 2 million years ago and has undergone genomic replication, chromosomal rearrangement, gene loss and transposition element amplification. These changes have led to significant differences among subgenomes (Pan et al., 2020). Among them, the amplification of transposition elements promotes genomic enlargement and also affects gene regulation and three-dimensional structure (Wang et al., 2021; 2022). 2.2 Key milestones in cotton genome sequencing projects In 2012, the first cotton D genome (G. raimondii) was released. Subsequently, the reference genomes of genome A (G. arboreum, G. herbaceum) and allotetraploid cotton (G. hirsutum, G. barbadense) were also completed successively, greatly promoting the research (Hu et al., 2019; Huang et al., 2020). In recent years, new technologies such as single-molecule sequencing, Hi-C and optical mapping have made gene assembly more complete, especially in high-repetition regions and centromere regions (Wang et al., 2018; Hu et al., 2019; Pan et al., 2020). Meanwhile, whole-genome resequencing, pan-genome and three-dimensional genome studies have revealed the diversity and regulatory networks of the cotton genome (Pan et al., 2020; Wang et al., 2022; Li et al., 2024). 2.3 Public databases and resources (CottonGen, CottonFGD, NCBI, Ensembl Plants, etc.) Cotton genome research relies on multiple databases and platforms (Pan et al., 2020): CottonGen: Integrated genomic, transcriptomic, variant, QTL and phenotypic data, providing multiple analytical tools. CottonFGD: Mainly used for functional genome annotation, including gene families, expression profiles and visualization tools. NCBI, Ensembl Plants: Provide genomic sequence, annotation and alignment tools for cotton and related species. These databases facilitate data storage, retrieval and sharing, enabling researchers to use genomic information more efficiently. 2.4 Challenges specific to cotton genomics (polyploidy, repetitive sequences). The cotton genome is highly polyploid and contains a large number of repetitive sequences. This brings great difficulty to assembly, annotation and mutation detection (Wang et al., 2018; Hu et al., 2019; Huang et al., 2020; Pan et al., 2020). The A and D subgenomes of allotetraploids have many homologous genes and structural variations, which can easily cause confusion in gene attribution and make expression regulation more complex. Furthermore, transpostion elements occupy the majority of the genome (more than 70% of the A genome), increasing instability and making annotation more difficult (Pan et al., 2020; Wang et al., 2021). Therefore, more efficient and precise bioinformatics tools are needed to enhance data parsing capabilities. 3 Categories of Bioinformatics Tools 3.1 Genome assembly and annotation High-quality assembly and annotation are the foundation for studying the cotton genome. Commonly used sequence alignment software includes Bowtie2 and BWA, and there are also some automated annotation platforms. CottonGen, CottonFGD and CottonMD integrate the reference genomes and annotation data of multiple cotton species and can be used for gene mapping, structural analysis and batch annotation (Yu et al., 2013; Zhu et al., 2017; Yang et al., 2020; 2022). 3.2 Comparative genomics and evolutionary analysis Comparative genomic tools (such as MCScanX, VISTA, and PLAZA) are often used to analyze homology and collinearity among different species or subgenomes, and can also be used to study evolutionary relationships. These analyses revealed gene family expansion, genome-wide replication and structural variations (Gao et al., 2017; Yang et al., 2020; Su et al., 2023). The CottonGen et al. Platform provides genomic alignment and genetic map comparison, facilitating the study of evolution and polyploidy (Yu et al., 2013; 2015; Yang et al., 2020).
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