Fat greenling (Hexagrammos otakii) is an important aquaculture fish species in northern China. Unfortunately, the increase of nitrogen in water due to residual feed and animal feces has caused considerable losses to the fat greenling breeding industry. Studies on detoxification metabolism and immune responses of fat greenling under ammonia stress have not been carried out. We used high-throughput sequencing to extract RNA from the liver of fat greenling, 48 and 96 h post-exposure, to water containing 30 mg/L NH₄Cl. A total of 87,675 high-quality unigenes were obtained by transcriptome analysis, the N50 and mean length were 1,523 and 772 bp, respectively. There were 320 and 272 genes (DEGs) identified in the two sampling times (48 and 96 h), containing 132 and 137 significantly up-regulated genes, and 188 and 135 down-regulated genes, respectively. Ten DEGs were randomly selected for validation by quantitative PCR. Further annotation and analysis indicated that the DEGs were enriched in the MAPK-signaling pathway, FOXO-signaling pathway, phosphatidylinositol-signaling pathway, cytokine-cytikine receptor interaction, Hippo-signaling pathway, and neuroactive ligand-receptor interaction. These pathways were mainly related to oxidative stress and immune responses. This research provides a valuable resource to further study of detoxification metabolism and immune responses of fat greenling under ammonia stress.

Fat greenling (Hexagrammos otakii Jordan & Starks, 1895) is a valuable marine fish species, crucial for aquaculture in Northern China due to its high-quality meat and significant economic value. However, the aquaculture industry faces challenges such as trait degradation, early sexual maturity, and disease susceptibility, necessitating advanced genomic interventions for sustainable cultivation. This study presents the first chromosomal-level genome assembly of H. otakii, achieved using PacBio long-read sequencing and Hi-C technology. The assembly yielded a genome size of 682.43 Mb with a contig N50 size of 2.39 Mb and a scaffold N50 size of 27.83 Mb. The completeness of genome assessed by BUSCO is 96.99%. A total of 22,334 protein-coding genes were predicted, with 21,619 (96.80%) functionally annotated across various protein databases. This genomic resource is a step forward in supporting the breeding, germplasm conservation, and enhancement of H. otakii, facilitating genetic studies and the development of strategies for disease resistance and growth optimization in aquaculture.

Hexagrammos otakii, also commonly called “Fat Greenling”, is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of H. otakii, generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the H. otakii genome, followed by microsatellites. In the phylogenetic tree, H. otakii was placed within a well-supported clade (bootstrap support = 100%) that included S. sinica, N. coibor, L. crocea, and C. lucidus. PSMC analysis revealed that H. otakii underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (~70–15 Kya), with no significant recovery observed by ~10 Kya. This study was a comprehensive genome survey analysis of H. otakii, providing insights into its genomic characteristics and population dynamics.