International Journal of Marine Science, 2025, Vol.15, No.5, 233-244 http://www.aquapublisher.com/index.php/ijms 235 genome, mainly including two major categories: equilibrium variation and non-equilibrium variation. Equilibrium SVs such as inversion and translocation refer to the inversion or exchange of chromosomal fragments, but the total copy number of genomes has not changed; non-equilibrium SVs include deletion, insertion, and duplication, which can cause changes in gene dosage. A deletion of a sequence may cause several genes to be lost, and insertion may add exogenous or repeat sequences, while duplications (including tandem and dispersed repeats) may lead to an increase in copy number of genes or regulatory elements. In addition, large-scale copy number variation (CNV) is sometimes listed alone, usually referring to an increase or decrease in the number of fragments relative to the reference genome, which can be regarded as a general term for deletion and amplification (Pettersson, 2019). The distribution of structural variations in the genome is not uniform, and their size can range from 50 bp to millions of bp, and their effects on genes also vary according to their location. The SV that occurs in the coding region may interrupt the open reading frame or alter the coding sequence, thereby directly altering protein function. Figure 1Ctenoides ales and summary of its genome assembly (Adopted from McElroy et al., 2024) Image caption: (A) Adult Ctenoides ales in aquarium setting, flashing light display visible in middle individual. Image credit: Jeanne M Serb. (B) Hi-C contact map for C. ales, highlighting the 18 chromosomes recovered from the genome assembly. Darker red indicates higher density of contact, blue and green boxes denote chromosome and contigs, respectively. (C) Snail plot summarizing key assembly statistics for final C. ales assembly with BUSCO results (Adopted from McElroy et al., 2024) 3.2 Application of high-throughput sequencing and long-reading technology in SV detection Since structural variations usually involve large fragment sequence changes, it is difficult for traditional molecular markers and PCR methods to detect them globally. The development of high-throughput sequencing technology provides a revolutionary means for SV detection. Based on the data of second-generation sequencing short read lengths, genomic structural variation can be predicted through strategies such as paired-end mapping, read length alignment spacing abnormalities and sequencing depth analysis. However, the limitation of short read length makes it less effective when resolving large SVs in complex or repetitive areas (Romagnoli et al., 2023). With the advent of third-generation sequencing, long read length sequencing (such as PacBio and Oxford Nanopore technologies) can generate ultra-long read lengths of tens of thousands to millions of bases. These read lengths cover many repeating sequence areas where short read lengths cannot be uniquely aligned, greatly improving the sensitivity to detection of large or complex structural variations. It is reported that a single mammalian genome can detect more than 20 000 to 30 000 SVs using long-read-length technology, which is 3 to 6 times that of short-read-length detection. In oyster research, the application of long-read long-read technology has also achieved remarkable results. Yildiz et al. (2022) integrated a variety of alignment and variation detection tools to
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