Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, 53334, Korea.
Department of Bio-AI Convergence, Chungnam National University, Daejeon, 34134, Republic of Korea.
Sci Data. 2024 Nov 4;11(1):1193. doi: 10.1038/s41597-024-04033-1.
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.
橄榄石斑鱼（Paralichthys olivaceus），又称韩国牙鲆，是东亚国家具有重要经济价值的一种比目鱼。在这里，我们利用高保真长读测序和其双亲短读测序数据，为两个不同的橄榄石斑鱼个体提供了四个完全分相的基因组组装。我们获得了 42-44GB 的约 15-kb 和 ~Q30 高保真长读，其组装质量值约为 53。我们为每个基因组组装注释了约 30K 个基因、约 170-Mb 重复序列和约 3M 5-甲基胞嘧啶位置，并建立了橄榄石斑鱼基于图的草图泛基因组。我们鉴定了 5M 个单核苷酸变异和 100K 个结构变异及其基因型信息，其中约 13%的变异可能在这两个韩国个体中固定。基于我们的染色体水平基因组组装，我们还探索了 Pleuronectiformes 科的染色体进化，正如之前报道的那样。我们高质量的基因组资源将有助于未来的基因组选择，以加速橄榄石斑鱼的选育过程。
