Abstract
<title>Abstract</title> <p> The Argentine hake ( <italic>Merluccius hubbsi</italic> ) is a cornerstone species of the Southwest Atlantic marine ecosystem and one of the most valuable fishery resources of the region. Despite its economic and ecological importance, comprehensive genomic resources for this species remain scarce, limiting the understanding of its evolutionary history and population dynamics. Here, we present the first high-quality, <italic>de novo</italic> genome assembly of <italic>M. hubbsi</italic> utilizing a hybrid sequencing strategy combining PacBio Sequel long reads and NovaSeq short reads (~112X coverage). The polished assembly spans approximately 425.3 Mb and facilitated the successful annotation of 28,998 protein-coding genes. A time-calibrated Bayesian phylogeny resolved the biogeographic history of the genus, dating its origin to the late Oligocene (~34 MYA) and positioning <italic>M. hubbsi</italic> as a crucial Miocene-diverging lineage linking the Atlantic and Pacific radiations. Furthermore, genomic population analyses revealed remarkable genetic health. Runs of homozygosity (ROH) analysis demonstrated an almost complete absence of recent inbreeding ( <italic>F</italic> <sub> <italic>_ROH</italic> </sub> < 0.01%), reflecting a massive, panmictic population with high gene flow. Finally, Pairwise Sequentially Markovian Coalescent modeling traced the species demographic history, revealing a stable historical effective population size ( <italic>N</italic> <sub> <italic>_e</italic> </sub> ) that peaked around 100,000 years ago before experiencing a contraction coinciding with the Last Glacial Period. Overall, these findings indicate that <italic>M. hubbsi</italic> maintains robust genetic diversity despite historical climate fluctuations and intense contemporary fishing pressure. This reference genome provides an invaluable resource for future studies on stock assessment, functional adaptation, and the sustainable management of marine fisheries. </p>