International Journal of Molecular Zoology, 2025, Vol.15, No.2, 58-68 http://animalscipublisher.com/index.php/ijmz 61 3.2 Genomic distribution and hotspots of SVs Structural variations (SVs) are often enriched in genomic regions containing repetitive sequences, such as fragment repeats and transposition elements. These elements can mediate chromosomal rearrangement and promote the formation of SVS (Mostovoy et al., 2021; Laufer et al., 2023). However, during the comparison process of these regions, ambiguity is prone to occur, and the accurate detection of SV faces challenges. However, with the advancement of long-read sequencing technology and optical mapping methods, the resolution of these complex regions has been improved (Mostovoy et al., 2021; Smolka et al., 2024). Due to high repeatability and structural complexity, the centromere and telomere regions have become hotspots of structural variation, and these characteristics make them more prone to rearrangement. In recent years, the development of sequencing and assembly technologies has enabled these previously hard-to-obtain information regions to be analyzed more accurately, thereby revealing their important roles in genomic evolution and diversity (Laufer et al., 2023). 3.3 Population-level SV diversity Population-scale studies have shown that structural variations (SVs) exhibit significant diversity among different geographical populations, and certain variations have unique frequency and distribution characteristics in specific populations (Merot et al., 2020; Ebert et al., 2021; Mostovoy et al., 2021). High-throughput sequencing technology and haplotype resolution sequencing methods are helpful for identifying common and rare SVS, providing tools for studying their evolutionary significance and adaptive functions (Ebert et al., 2021; Mostovoy et al., 2021). In the frontier region of invasion and expansion, some structural variations are unique to specific populations (private variations), while others are shared by multiple populations. This reflects the combined effect of recent population dynamic events and historical gene flows (Merot et al., 2020; Ebert et al., 2021). The identification of private and shared structural variations helps to reveal the adaptation mechanisms and evolutionary dynamics of invasive species. 4 Functional Impact of Structural Variations 4.1 SVs affecting gene regulation and expression Structural variations (SVs) may disrupt promoters or reposition enhancers, thereby causing significant changes in gene expression. SVs are enriched in enhancers and other regulatory element regions. Their presence can directly alter gene regulatory mechanisms, and usually have a greater impact on gene expression than single nucleotide variations (Chiang et al., 2016). When SVs disrupt the promoter or enhancer regions, it may disrupt the enhancer-promoter interaction and affect the stability and variability of gene expression between cells (Weintraub et al., 2017; Schoenfelder and Fraser, 2019). SVs can also form fused transcripts or new regulatory elements by connecting originally isolated genomic regions. These rearrangements may introduce new regulatory sequences (such as enhancers or promoters) into different genomic environments, resulting in abnormal or new gene expression patterns (Chiang et al., 2016; Andersson and Sandelin, 2019). Such events may either endow adaptive traits or lead to adverse phenotypic changes. 4.2 SV and transposable element interactions Transposition elements (TEs) are commonly found in SV insertion hotspots and are important factors leading to genomic instability and structural rearrangement (Weintraub et al., 2017; Judd et al., 2020). TEs can serve as a source of new regulatory sequences (such as enhancers and promoters), and their active transfer can promote the generation of SVS that affect gene regulation (Sundaram and Wysocka, 2020). TEs and SVs co-evolve, with the former providing cis-regulatory innovations, and the latter reshaping chromatin structure. This interaction can promote the formation of species-specific regulatory networks, and gene expression differences, as TEs are "requached" as functional enhancers or promoters, while SVs change their positional background in the genome (Sundaram and Wysocka, 2020).
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