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

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.