International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3, 111-122 http://ecoevopublisher.com/index.php/ijmec 114 2.3 Ecological significance of Spanish mackerel adaptive evolution Understanding the adaptive evolution of Spanish mackerel is of great significance for assessing its ecological status and ability to cope with environmental changes. On the one hand, the evolutionary ability of Spanish mackerel to adapt to a changing environment (such as seasonal changes in water temperature and salinity) determines whether its population can maintain stability in the context of climate change and habitat changes. For example, the rise in water temperature and changes in ocean current patterns in the western Pacific in recent years have had an adverse impact on the reproduction and survival of Japanese Spanish mackerel (Yang et al., 2022). On the other hand, as a high-trophic-level predator, the evolutionary adaptation of Spanish mackerel will also have a chain effect on the downstream ecology-for example, changes in Spanish mackerel predation pressure may affect the succession of pelagic fish populations. In the context of current global change, research on Spanish mackerel adaptive evolution also has important resource management significance. If genetic variations related to key traits such as stress resistance and fecundity can be identified in the Spanish mackerel genome, it will help predict the potential response of its population to environmental changes (such as rising sea temperatures and changes in salinity). In addition, there may be genetic differentiation and local adaptation between Spanish mackerel populations in different sea areas. If these differences are not understood and unified management is carried out, some hidden populations may be overexploited or neglected. Population genomics studies have shown that even if the overall gene exchange of marine fish is frequent and high gene flow may mask local adaptation signals, some fine genetic structure and adaptive differences may still exist. 3 Research Progress on the Spanish mackerel Genome 3.1 Genome sequencing and assembly research Thanks to the development of high-throughput sequencing technology, Spanish mackerel genome sequencing has made breakthrough progress in recent years. In 2024, researchers constructed the chromosome-level reference genome of the Spanish mackerel genus for the first time, with the Indo-Pacific Spanish mackerel (Scomberomorus guttatus) as the object. The total size of the genome is about 798 Mb, which is assembled into 24 pseudo-chromosomes, with a Scaffold N50 of 32.9 Mb and a Contig N50 of 8.84 Mb. Gene prediction obtained about 25,886 protein-coding genes. This is the first high-quality genome sequence of the Spanish mackerel genus, laying the foundation for in-depth research on the genome evolution of fish in this genus. Liu et al. (2025) constructed a high-quality reference genome of the Japanese Spanish mackerel (S. niphonius) and explored its population structure in combination with population resequencing data. The acquisition of the Japanese Spanish mackerel genome fills the gap in Spanish mackerel genetic resources in East Asia and creates conditions for comparing the similarities and differences of the genomes of different Spanish mackerel species. In the process of assembling the Spanish mackerel genome, researchers usually use the strategy of third-generation long-read sequencing combined with Hi-C assisted assembly to ensure the continuity and accuracy of the assembly. For example, in the study of the Indian-Pacific Spanish mackerel genome, PacBio HiFi read-length sequencing was used to obtain high-precision long fragment sequences, and the assembled Contig was anchored to the chromosomes in combination with Hi-C spatial conformation capture, achieving the assembly of 24 chromosomes. It is worth mentioning that through the comparison of high-quality genomes, some evolutionary characteristics of the Spanish mackerel genome can be found. For example, about 36% of the Indian-Pacific Spanish mackerel genome is repeated sequences, and the genome is highly continuous (Bayona-Vásquez et al., 2017; Zheng et al., 2017). 3.2 Progress in comparative genomics Comparative genomics studies of Spanish mackerel mainly focus on comparing genomic characteristics and evolutionary laws within the Scombridae family and with other pelagic fish. On the one hand, within the Scombridae family, by comparing the genomes of Spanish mackerel with those of tuna, mackerel, etc., shared and unique genomic changes can be identified. For example, Machado et al. (2022) constructed the genome of Atlantic mackerel and pointed out that as an important pelagic fish, it is comparable to Spanish mackerel in terms
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