International Journal of Marine Science, 2025, Vol.15, No.2, 53-64 http://www.aquapublisher.com/index.php/ijms 56 4.2 Transposable elements and repetitive sequence content The grouper genome contains a large number of repetitive sequences. In yellow grouper, repetitive sequences account for 41.17% of the entire genome (Zhang et al., 2024). There is currently no detailed classification of transposable elements (TE) types, but repetitive sequences are common in the grouper genome. This suggests that transposable elements and other repetitive sequences play an important role in the formation of genome structure, which can promote grouper genome evolution and species diversification (Zhou et al., 2019; Yang et al., 2021; Li et al., 2024; Zhang et al., 2024). 4.3 Structural variation: CNV, inversion and segmental duplication Structural variation (SV) is a very common phenomenon in groupers and an important reason for the genetic differences between different grouper species. Yang et al. (2023) found 46 643 variations (SV) in their study of the genome of Shanghai-Long hybrid grouper (E. fuscoguttatus ×E. lanceolatus), some of which were closely related to genes such as metabolism, cell cycle and growth. When they conducted a colinearity analysis on brown grouper, they did not find large-scale chromosome duplications, but found that its colinearity with closely related species was still high, indicating that the chromosomes were stable as a whole, but there were some local variations that may be related to adaptability (Yang et al., 2021; Yang et al., 2023). Wang et al. (2022) also observed copy number variation (CNV) and gene duplication in some other grouper species, such as potato grouper. In this grouper, the number of copies of Gh and Hsp90b1 genes is higher, which may be related to characteristics such as rapid growth and stress resistance. 4.4 Dynamic changes in mitochondrial and nuclear genomes The mitochondrial genome of grouper is relatively conservative, and it usually contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Due to duplication events, new gene arrangements appear in the mitochondrial genome of some grouper species (Zhuang et al., 2013; Kundu et al., 2024). Zhuang et al. (2013) found additional tRNA genes in some grouper genera, which is a unique evolutionary event. Mitochondrial genes are usually subject to strong purifying selection, among which rRNA and tRNA genes are the most conservative, while non-coding regions and some protein-coding genes (such as ND6, ATP8) have relatively large variations (Zhuang et al., 2013; Kundu et al., 2024). In contrast, the structure of the grouper nuclear genome is more complex and more variable, including variation values (SVs) and gene family expansions, while these differences are less obvious in the mitochondrial genome (Figure 2) (Zhou et al., 2019; Yang et al., 2021; Wang et al., 2022; Yang et al., 2023; Li et al., 2024; Zhang et al., 2024). 5 Speciation Mechanisms of Groupers 5.1 Allopatric and sympatric speciation in coral reef habitats Grouper species can form both allopatrically and sympatrically, particularly in coral reef environments in the Indo-Pacific and Tropical Atlantic + Eastern Pacific (TAEP) regions. Allopatric speciation is often caused by large-scale geological events, such as the uplift of the Isthmus of Panama and crustal movements, which created physical barriers that allowed grouper species to diverge. In contrast, sympatric speciation occurs in places like the Indo-Australian Archipelago (IAA), where species diverge in the same area, often due to differences in habitat preferences and ecological specialization. These divergences have accelerated the diversification of groupers in coral-rich areas, such as the Abu Dhabi Bay in the Indian Ocean and the Caribbean Sea. Although these places are places where species aggregate, they are not the main origins of species (Cao et al., 2014; Cao et al., 2022). 5.2 Geographic isolation and the role of ocean currents Geographic isolation, usually caused by geological movements and sea level changes, has played a major role in the differentiation of grouper species. Taking the Isthmus of Panama as an example, its formation led to the isolation of grouper populations, thus forming allopatric species. Changes in ocean currents can also affect the dispersal of juveniles and the connection between populations, which further accelerates the regional differentiation of genetic structure. The drop in sea level during the ice age can also isolate populations, leading to lineage differentiation and population bottleneck effects. Although there is a lot of gene flow within the region,
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