Cotton Genomics and Genetics 2025, Vol.16, No.6, 259-268 http://cropscipublisher.com/index.php/cgg 260 2 Genomic Landscape of Structural Variations in Cotton 2.1 Advances in sequencing technologies enabling SV detection To truly understand the appearance of the cotton genome is not something that can be achieved at the very beginning. Although early sequencing technology solved the problem of "being able to see", it was far from being able to "see clearly". Especially those regions rich in repetitive sequences and close to the filaments have almost become blind spots where scientists have no idea where to start. It was not until recent years that the situation gradually began to improve. Technologies such as single-molecule real-time sequencing (SMRT), BioNano optical spectroscopy and Hi-C have been integrated and applied successively. Finally, the reference genomes of Gossypium hirsutum and Gossypium barbadense were fully pieced together (Chang et al., 2024). Those vague fragments of the past, the parts that were once unpieced together or simply ignored, have finally revealed their details this time. Subsequently, the addition of Oxford nanopore and the PacBio platform further enhanced the resolution, enabling the identification of even complex structures such as large areas of inversion and centromere repositioning. It is worth noting that the significance of these advancements goes far beyond the "more comprehensive" data. For the first time, they have enabled us to truly understand the structural differences between different lineages, and have also made comparative genomic research on cotton more solid and convincing. 2.2 Types and frequency of SVs in cotton genomes The genome of cotton is no quiet world, where various variations occur one after another: insertions, deletions, inversions, translocations, copy number changes-they can be found on almost every chromosome. Studies have found that some variations are so extensive that they span large areas between or within the arms and can affect hundreds of genes at one time (Meng et al., 2023). Among these chromosomes, A08 is particularly special, with approximately one-third of the regions undergoing structural variations, often accompanied by recombination or gene loss. Meanwhile, genome-wide analysis also revealed tens of thousands of lineage-specific SNPS and SVS, which gradually widened the functional gap between upland cotton and island cotton. It should be noted that the distribution of variations is not uniform: some areas are like ignited "hotspots", with dense variations; Some areas, however, remain almost motionless, perhaps being "quiet zones" left over from long-term domestication or selection under pressure. This interwoven genomic pattern of cold and hot makes the evolutionary process of cotton not monotonous; instead, it is more like a dynamic map that is constantly being rewritten. 2.3 Comparative genomic analyses reveal lineage-specific SVs If the differences between land cotton and island cotton are understood as a simple sequence rearrangement, it is obviously an underestimation of their complexity. After polyploidy, long-term domestication and natural selection have continuously left traces at the genomic level-large fragment inversions, translocations, and even centromeric repositioning have occurred successively during this period (Fan et al., 2020). These changes, layer upon layer, gradually reshaped the way genes were organized and also widened the gap in traits. Some variations are related to the expansion or expression bias of gene families, and ultimately manifest as differences in agronomic traits such as fiber quality and stress resistance. From a deeper perspective, structural variations seem to be involved in the evolution of centromeres and also affect the overall stability of the genome. Different families of repetitive sequences have formed their own independent centromeric structures in each subgenome, causing the two species to also present a pattern of "each going its own way" at the chromosomal level. It can be said that in the differentiation process of upland cotton and Pima cotton, structural variation was not an accidental side branch but a driving force that accompanied them all the way. 3 Functional Impact of SVs on Gene Expression and Regulation 3.1 SVs alter gene dosage and copy number Sometimes, changes in gene expression are not caused by mutations themselves, but by alterations in the "quantity". Structural variations (SVs) such as insertions, deletions or duplications can directly change the gene dose or copy number, thereby pulling up or down the expression level. This phenomenon is not uncommon in cotton (Cheng and Zhang, 2025). Studies have found that hundreds and thousands of genes are affected by structural variations. Some genes disappear due to regional loss, while new genes emerge due to repetitive or
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