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Xuan B, Park J, Choi S, You I, Nam BH, Noh ES, Kim EM, Song MY, Shin Y, Jeon JH, Kim EB. Draft Genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle. G3-GENES GENOMES GENETICS 2021; 11:6263857. [PMID: 33944944 PMCID: PMC8496316 DOI: 10.1093/g3journal/jkab147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
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.
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Affiliation(s)
- Biao Xuan
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Sukjung Choi
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Inhwan You
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Mi-Young Song
- Inland Fisheries Research Institute, National Institute of Fisheries Science, Gapyeong 12453, Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc, Yongin 16954, Republic of Korea
| | - Ji-Hyeon Jeon
- Research and Development Center, Insilicogen Inc, Yongin 16954, Republic of Korea.,Department of Biological Science, Sungkyunkwan University, Suwon 16419, Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
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Park J, Kim EB. Insights into the Gut and Skin Microbiome of Freshwater Fish, Smelt (Hypomesus nipponensis). Curr Microbiol 2021; 78:1798-1806. [PMID: 33738530 DOI: 10.1007/s00284-021-02440-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/01/2021] [Indexed: 12/19/2022]
Abstract
Freshwater smelt (Hypomesus nipponensis) is a planktivorous fish found in the river of South Korea, Japan, China, and Russia. Because of its specific characteristics living in the cold temperature, this species is economically valuable in the various countries that held winter festival. The body size of the smelt is too small, so people consumed raw smelt during the winter festival sometimes. However, the microbial studies of smelt are nonexistent. Here, we characterized and compared the bacterial communities in the gut and skin of freshwater smelts. We amplified, sequenced, and analyzed the V4 regions of bacterial 16S rRNA genes from freshwater smelts. The microbial diversity in the skin (375 OTUs) was much greater than that in the gut (250 OTUs). At the phylum level, Proteobacteria (gut: 51.5%; skin: 52.9%), Firmicutes (gut: 30.6%; skin: 25.4%), Bacteroidetes (gut: 7.7%; skin: 14.7%), and Actinobacteria (gut: 5.2%; skin: 3.8%) were predominant in both organs. At the genus level, Sphingomonas (gut: 24.9%; skin: 4.4%, P < 0.01) was more abundant in the gut, whereas Acinetobacter (gut: 0.8%; skin: 11.8%, P = 0.02) and Pseudomonas (gut: 0.3%; skin: 2.1%, P = 0.01) were more abundant in the skin. Both beneficial (Lactobacillus) and harmful (Staphylococcus and Streptococcus) bacteria were detected in both organs, even under freshwater conditions. These results revealed that smelts have their own unique microbial communities in the gut and skin. Our findings broaden the understanding of planktivorous freshwater fish microbiomes and provide new insights into fish microbiomes for ensuring food safety.
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Affiliation(s)
- Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Kangwon-do, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Kangwon-do, Republic of Korea. .,Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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