International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3, 111-122 http://ecoevopublisher.com/index.php/ijmec 115 of genome size and number of coding genes, both containing about 3 billion base pairs and about 30 000 genes. This suggests that the overall genome size and gene number of Scombridae fish are relatively close. However, through fine comparison, it can also be found that some genes have copy number variations or sequence differences between different lineages. For example, Havelka et al. (2021) reported a chromosome-level genome of a closely related species in the Scombridae family-tunas of the genus Euthynnus (such as Euthynnus affinis)-and annotated it using transcriptome data. On the other hand, comparing the Spanish mackerel genome with pelagic fish with very different environmental adaptations can help reveal the genomic basis of adaptive evolution. For example, tuna have a special adaptation of partial endothermic ability (increasing body temperature), and studies have found that some metabolic and muscle-related genes are expanding or evolving rapidly in the tuna genome (Ciezarek et al., 2020). At present, comparative genomics research on Spanish mackerel is still in its infancy, but existing studies have shown its application prospects. For example, by comparing the genomes of the Indo-Pacific Spanish mackerel with other fish, it was found that some unique repetitive sequences in its genome were suppressed inside tandem repeat genes. For another example, a comparison of the Spanish mackerel and mackerel genomes revealed that many chromosome fragments of the two were colinear, but there were also a few chromosome rearrangements and breaks. These variations may be related to adaptation to different ecological niches during their respective evolution (Li et al., 2025). 3.3 Current status of functional genomics research Functional genomics focuses on the level of gene expression and gene function, exploring how the genome plays a role in phenotypic adaptation. In the study of Spanish mackerel, functional genomics work mainly includes transcriptome analysis, proteome and epigenetic regulation research. At present, since Spanish mackerel is not a model organism, its functional genomics research is relatively limited, but initial progress has been made. In Spanish mackerel, some studies have begun to focus on the expression changes and selection patterns of functional gene families such as heat shock proteins and immune proteins under environmental stress, as well as the role of epigenetics in local adaptation of populations. For example, Lee et al. (2023) used single-molecule sequencing to simultaneously obtain DNA methylation information during the assembly of the Pacific mackerel genome. In the Indo-Pacific Spanish mackerel genome project, RNA from multiple tissues such as muscle, liver, spleen, and kidney was collected to construct transcriptomes to assist gene annotation. These transcription data not only improve the accuracy of gene prediction, but also lay the foundation for analyzing the expression characteristics of important functional genes. 4 Molecular Mechanisms of Adaptive Evolution of Spanish mackerel 4.1 Key genes related to environmental adaptation The ability of Spanish mackerel to adapt to the changing marine environment is inseparable from the role of a series of functional genes. The molecular mechanism of its environmental adaptation involves a multi-gene network, including cell stress defense (such as the HSP family), osmotic pressure regulation (ion transporters), energy metabolism and movement (mitochondrial function and muscle protein). At the genomic level, researchers are gradually identifying key genes and gene families related to adaptation to environmental factors such as temperature and salinity. For example, heat shock proteins (HSPs) play an important role in cellular stress response as molecular chaperones. Fish usually regulate salt balance in the body through ion transporters (such as Na^+/K^+-ATPase, ion channel proteins, etc.) expressed in gills and kidneys. Therefore, genes involved in ion transport and osmotic pressure regulation are crucial for Spanish mackerel to adapt to different salinity environments. Some studies have shown that in order to adapt to the extremely cold and low-oxygen environment, the hemoglobin genes of Antarctic fish have changed or even disappeared; in contrast, Spanish mackerel are in a warm and oxygen-rich environment, and may have evolved different blood oxygen transport strategies (Wang et al., 2025). 4.2 Evolutionary mechanisms of immunity and disease resistance There are many types of pathogens in the marine environment, and Spanish mackerel have also developed unique immune defense mechanisms during the long evolution process. A phylogenetic study of the complement system
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