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bioRxiv · 10.1101/2025.10.22.683973

Near telomere-to-telomere genome assembly of the Chilean jack mackerel Trachurus murphyi

Ferrada-Fuentes, S.·Quevedo, C.·Herrera-Yanez, V.·Canales-Aguirre, C. B.·Aguilera, F.
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Abstract

The Chilean jack mackerel (Trachurus murphyi) is an economically important pelagic fish widely distributed across the South Pacific Ocean. Due to intense fishing pressure and the lack of high-quality genomic resources, the development of sustainable fisheries management strategies has been hindered. Here, we present a near telomere-to-telomere genome assembly of T. murphyi using PacBio and Hi-C sequencing data. The assembled genome spans 818.31 Mb, with a contig N50 length of 24.89 Mb and a scaffold N50 length of 34.34 Mb. The assembly is anchored on 24 pseudo-chromosomes, covering 95.80% of the genome. BUSCO analysis indicates a high level of completeness at 99.0%, and telomeres and centromeres were identified on pseudo-chromosomes. Repetitive sequences account for 24.24% of the total genome, and 47,734 protein-coding genes were annotated, 90.98% of them with assigned function. Comparative genomics analyses reveal strong synteny with its congeneric Trachurus species. This high-quality genome assembly serves as a valuable resource for studying the genetic diversity and population structure of the Chilean jack mackerel and provides a solid foundation for future management and conservation efforts.

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Ferrada-Fuentes, S., Quevedo, C., Herrera-Yanez, V., Canales-Aguirre, C. B., Aguilera, F.. 2025-10-23. Near telomere-to-telomere genome assembly of the Chilean jack mackerel Trachurus murphyi. https://doi.org/10.1101/2025.10.22.683973

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