Genome-wide snp detection in the horse mackerel (trachurus trachurus, T. Mediterraneus, T. Picturatus) of turkish waters using illumina and nanopore sequencing

Abstract

The horse mackerel, distributed in the Pacific, Atlantic, Indian Ocean, and Mediterranean waters, is economically valuable due to its high nutritional content and fishing capacity. Global market demand for this species has been increasing over the years. This rising demand causes fishing pressure, endangering the species' sustainability. Especially the horse mackerel species (Trachurus trachurus, Trachurus mediterraneus and Trachurus picturatus), which are found as mixed stocks in Turkish waters and under fishing pressure, should be considered as different stocks and evaluated with distinct management strategies. However, due to the difficulty of distinguishing these three Trachurus species based on morphological characteristics, conflicting reports have emerged, particularly regarding their distribution areas, and species identification is not always precise. In our study, we sequenced the genomes of these species using next-generation sequencing (Illumina) and third-generation sequencing technologies (Oxford Nanopore), and identified SNP (single nucleotide polymorphism) differences to distinguish the species. We identified a total of 2311386 SNPs in the Trachurus trachurus genome, of which 1313612 were transitions and 997774 were transversions. 5099766 SNPs in the Trachurus picturatus genome, of which 2927066 transitions and 2172700 transversions. Similarly, 5007863 SNPs in the Trachurus mediterraneus genome, of which 2940560 transitions and 2067303 transversions. These SNP datasets provide a robust genetic marker toolkit for accurately distinguishing Trachurus species and evaluating genetic diversity within and between populations. The findings of this study contribute essential genetic resources for defining the stock structures of these species, informing sustainable fisheries management strategies, and guiding conservation initiatives. By addressing the challenges of species identification and genetic diversity assessment, this research lays the groundwork for mitigating the impact of overfishing and ensuring the sustainability of horse mackerel populations in Turkish and global waters.