The olive flounder, Paralichthys olivaceus, also known as the Korean halibut, is an economically important flatfish in East Asian countries. Here, we provided four fully phased genome assemblies of two different olive flounder individuals using high-fidelity long-read sequencing and their parental short-read sequencing data. We obtained 42–44 Gb of ~15-kb and ~Q30 high-fidelity long reads, and their assembly quality values were ~53. We annotated ~30 K genes, ~170-Mb repetitive sequences, and ~3 M 5-methylcytosine positions for each genome assembly, and established a graph-based draft pan-genome of the olive flounder. We identified 5 M single-nucleotide variants and 100 K structural variants with their genotype information, where ~13% of the variants were possibly fixed in the two Korean individuals. Based on our chromosome-level genome assembly, we also explored chromosome evolution in the Pleuronectiformes family, as reported earlier. Our high-quality genomic resources will contribute to future genomic selection for accelerating the breeding process of the olive flounder.

Polypterus senegalus is a fish species characterized by primitive traits and unique physiological-anatomical features, representing a transitional stage toward terrestrial vertebrates. Diverging from other ray-finned fishes approximately 420 million years ago, it serves as a key model for vertebrate evolutionary studies. In this study, we identified 19,295 unique P. senegalus transcripts using Pacific Biosciences Iso-Seq, with most classified as novel exon combinations, intron retentions, or novel start and stop codons. This high-quality, full-length transcriptome revealed previously unreported isoforms and investigated their functional roles to enhance our understanding of the genomic complexity and evolutionary traits of the species. Notably, these isoforms were identified in genes associated with Polypterus's distinctive features, including limb flexibility (ACTN3B, MYBPC1), lung function (FAM13A, ERBB2, TCF7), and circulation (FBN1, MYH11B, MEF2CB). These findings offer molecular insights into early vertebrate terrestrial adaptation and the functional integration of key tissues in extant species.

The Korean cattle breed, Hanwoo, has been selected as a meat cattle breed since the late 1980s in Korea, but has suffered from reduced genetic diversity due to repeated selection within a single population. In this study, we generated high-fidelity long-read sequencing data (~Q30, 98–146 Gb) for three Hanwoo Research Center (HRC) Hanwoo individuals from early, intermediate, and current breeding generations of the genetically distinct HRC population. These datasets yielded four partially phased genome assemblies of early and intermediate generations and two fully phased genome assemblies of the current generation. Furthermore, we construct a graphical pangenome reference by combining 19 publicly available cattle assemblies with our six new assemblies, identifying 39.3 M single-nucleotide variants (SNVs) and 60.7 K structural variants (SVs). Among these, 27.8 K SNVs and 26 SVs were uniquely found in the HRC Hanwoo population. These high-quality genomic resources provide valuable insights into the genetic characteristics of HRC Hanwoo and will facilitate future breeding strategies and genetic improvement efforts.

Journal of Animal Science and Technology (JAST) is a peer-reviewed, open access journal publishing original research, review articles and notes in all fields of animal science. Topics covered by the journal include: genetics and breeding, physiology, nutrition of monogastric animals, nutrition of ruminants, animal products (milk, meat, eggs and their by-products) and their processing, grasslands and roughages, livestock environment, animal biotechnology, animal behavior and welfare.