Cotton Genomics and Genetics 2025, Vol.16, No.5, 210-221 http://cropscipublisher.com/index.php/cgg 211 of humans, this interaction pattern has been constantly strengthened or changed, ultimately influencing their genomic structure and trait expression today. Ultimately, cotton is actually an ideal "observation window" for studying polyploidy, subgenomic dominant expression, and even changes in genetic mechanisms (Mei et al., 2004; Wang et al., 2017). For this reason, we have decided to systematically sort out the research progress on the cotton pan-genome in recent years. This research will approach from three perspectives: First, the genetic diversity map brought about by pan-genome and structural variations; The second is the regulatory mechanism behind the asymmetry of subgenomic dominance and expression in polyploid cotton; Thirdly, how these discoveries can help us better understand the evolutionary process of plant genomes and even guide practical breeding, especially in improving fiber quality, increasing yield and resistance. Another point worth mentioning is that we will also combine some integrated cases from genomics, transcriptomics and epigenetics, attempting to illustrate from a multi-omics perspective that the pan-genome is not only about "discovering more", but is also gradually reshaping our overall understanding of cotton biology and providing new breakthroughs for precise improvement. 2 The Cotton Genome Landscape 2.1 Genome structure and evolution in diploid and polyploid cotton species Among the cotton genus plants, there are quite a few species-approximately 45 diploids and 7 allotetraploids. This quantitative diversity is underpinned by differences in genomic structure, especially between the A genome and the D genome. The volume of the A genome is almost twice that of the D genome. This difference is mainly not due to an increase in genes, but rather the proliferation of transposition factors (Pan et al., 2020). But if you think they are far apart, that's not entirely the case. The A and D genomes are generally consistent in terms of gene arrangement sequence and collinearity (Page et al., 2013), indicating that the parts that make the genome "larger" are mostly repetitive sequences rather than the core gene content. When it comes to heteropolyploids, such as upland cotton and island cotton, their emergence is not a "recent event"-dating back approximately one to two million years. AT that time, the A and D genomes of the ancestors combined and eventually left the "traces" of the AT and DT subgenomes in one cell nucleus (Hu et al., 2019). However, this kind of combination is not a "harmonious" matter. After polyploidy, it is often accompanied by chromosomal structural disorder, such as inversion, translocation, etc. Duplicated genes do not necessarily "stay well"-some retain the original function, some lose it, and some simply develop new functions (Li et al., 2016). 2.2 Role of polyploidization in shaping gene content and genome complexity The reason why the genome of cotton is becoming increasingly complex is, in most cases, closely related to the issue of "polyploidy". However, this was not caused by a single mutation; it has gone through several rounds of evolution. Such as sixfold transformation was an earlier event, and then there was another tenfold transformation that occurred in the later stage of evolution (Strygina et al., 2020). This repeated doubling of the genome not only increases the number of genes, but also has a deeper impact on gene regulation-the operation mode of the entire "control system" changes accordingly. But changes are not always symmetrical or fair. Some subgenomes have greater say in certain traits and show "dominance", such as being more easily expressed; Some, however, remain relatively low-key and less active. This bias causes the expression levels of certain genes to be significantly higher than those of others. Meanwhile, the chromatin structure may also have undergone a rearrangement. For instance, the improvement of traits such as fiber quality is likely related to higher expression of certain subgenomes (Figure 1) (Chen et al., 2020; Huang et al., 2021; Han et al., 2022). Of course, not all such "biased expression" is necessarily a good thing. Whether it is good or not depends on which gene it affects and what the environmental conditions are like. 2.3 Comparative genome assemblies of key cotton cultivars and wild relatives To understand exactly where modern cultivated cotton came from, it's no use just focusing on one variety. You need to bring along its "relatives" to take a look together. Especially those wild relatives, they actually contain a lot of genetic information that has been "filtered" out by modern varieties. With the advancement of sequencing technology, representative species such as upland cotton, island cotton, Asian cotton, and Raymond cotton now
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