Abstract

The Jonah’s icefish Neopagetopsis ionah is endemic to the frigid, oxygen-rich waters of the Southern Ocean. This species has evolved remarkable genetic and physiological adaptations, notably the loss of functional hemoglobin, making it an exemplary vertebrate model for studying evolutionary loss is gain and adaptation to extreme environments. In this study, we present a chromosome-level genome assembly of N. ionah (1.27 Gb) integrating Illumina, PacBio HiFi, and Hi-C sequencing data. The assembly comprises 24 chromosomes, with an anchoring efficiency of 96.8%. Genome annotation revealed that 42.14% of the genome consists of repetitive elements and identified 31,777 protein-coding genes. The high genomic collinearity with related species corroborates the assembly’s accuracy at the macroscale. This high-quality reference genome provides a crucial resource for elucidating the genetic basis of cold adaptation, trait loss, and the unique cardiovascular innovations in Antarctic icefish.