Draft genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle

Abstract

Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species and a winter economic aquaculture resource in South Korea. Because of its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summers. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) vs. warm (HT, 23°C) conditions to identify heat stress-induced genes and gene categories. We observed a total of 1987 contigs with N50 of 0.46 Mbp, with the largest contig (3.03 Mbp) in the assembled genome. A total of 20,644 protein-coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology terms and 11,560 genes for KEGG Orthology. We conducted the lost and gained genes analysis compared with three species that: human, zebrafish, and salmon. In the lost genes analysis, we detected that smelt lost 4461 (22.16%), 2825 (10.62%), and 1499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed that smelt gained 1133 (5.49%), 1670 (8.09%), and 229 (1.11%) genes compared with the above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with a false discovery rate <0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that upregulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and genes were downregulated by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, upregulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001), and calcium-release channel activity (GO:0015278, P < 0.01), and genes were downregulated for a nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of molecular mechanisms and heat responses and be useful for predicting survival of the smelt and its closely related species under global warming.

Keywords: Hypomesus nipponensis; genome; heat stress; high temperature; transcriptome.

Figure 1

Annotation and functional classification of unigenes in the genome of H. nipponensis. (A) Blast top 10 hit species. (B) GO analysis was performed at level 2 for the three main categories (BP, CC, and MF). (C) Pathway assignment based on the KEGG database. Unigenes were classified into seven main categories (A: Genetic Information Processing; B: Metabolism; C: Organismal Systems; D: Cellular Processes; E: Human Diseases; F: Environmental Information Processing; G: Brite Hierarchies).

Figure 2

Differential expression of high temperature in H. nipponensis vs. low temperature. (A) DEGs in the liver of female fish. (B) DEGs in muscle of female fish. (C) DEGs in the liver of male fish. (D) DEGs in muscle of male fish. The dots above the dotted line are FDR < 0.05, |log2FC| ≥ 1.

Figure 3

An overview of the KEGG pathway significantly enriched in DEGs in the (A) liver, and (B) muscle. The specific pathways are plotted along the y-axis, and the x-axis indicates the enrichment factor. The colored dots indicate the number of significant DEGs associated with each corresponding pathway: pathways with larger-sized dots contain a higher number of genes. The color of the each dot indicates the corrected P-value for the corresponding pathway.