Complete mitochondrial genome sequence and SNPs of the Korean smelt<i>Hypomesus nipponensis</i>(Osmeriformes, Osmeridae)

Choi, Suk-Jung; Kim, Eun Bae

doi:10.1080/23802359.2019.1613178

Cited by 4 publications

(3 citation statements)

References 6 publications

(7 reference statements)

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“…One non-native fish of interest in the estuary is the Wakasagi, also commonly referred to as the Japanese Pond Smelt (Hypomesus nipponensis, hereon "Wakasagi"). Wakasagi are widely distributed from the Kuril Islands of Russia and coastal regions and lakes of Japan to the South Korean Peninsula (Katayama et al 2001;Ilves and Taylor 2008;Choi and Kim 2019). In Japan, Wakasagi support a commercial freshwater fishery supported by an aquaculture program with annual hatchery releases of >10 billion eggs and newly hatched larvae into lakes and reservoirs (Nakamura and Watanabe 2001).…”

Section: Introductionmentioning

confidence: 99%

Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt

Davis¹,

Adams²,

Lewis³

et al. 2022

SFEWS

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Intentional introductions of non-native fishes can severely affect native communities. Wakasagi (Hypomesus nipponensis, referred to as Japanese Pond Smelt) are native to Japan and were once separated from their non-native congener the endangered Delta Smelt (Hypomesus transpacificus) of the San Francisco Estuary (hereon “estuary”) of California. Wakasagi were introduced into California reservoirs in the 20th century as forage fish. Wakasagi have since expanded their distribution downstream to the estuary, but less is known about Wakasagi’s current distribution status, biology in the estuary, and negative influences on Delta Smelt. In this study, we took a comparative approach by synthesizing long-term field monitoring surveys, modeling environmental associations, and quantifying phenology, growth, and diets of Wakasagi and Delta Smelt to describe abundance and range, trends of co-occurrence, and shared ecological roles between smelt species. We found Wakasagi in greatest abundance in the upper watershed below source reservoirs, and in the northern regions of the estuary with the most co-occurrence with Delta Smelt; however, their range extends to western regions of the estuary, and we found evidence of an established population that annually spawns and rears in the estuary. We found these smelt species have similar ecological roles demonstrated by overlaps in habitat use (e.g., an association with higher turbidities and higher outflow), phenology, growth, and diets. Despite similarities, earlier hatching and rearing of Wakasagi during cooler months and reduced growth during warmer drought years suggest this species is unlike typical non-natives (e.g., Centrarchids), and they exhibit a similar sensitivity to environmental variability as Delta Smelt. This sensitivity may be why Wakasagi abundance remains relatively low in the estuary.

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Section: Introductionmentioning

confidence: 99%

Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt

Davis¹,

Adams²,

Lewis³

et al. 2022

SFEWS

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show abstract

“…Smelt is an anadromous species ( Saruwatari et al 1997 ), but now it is cultivated in many reservoirs in South Korea. In a previous study, smelt samples from South Korea were identified as H. nipponensis ( Choi and Kim 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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

Xuan

Park

Choi

et al. 2021

G3 Genes|Genomes|Genetics

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Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. 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) versus warm (HT, 23 °C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50 of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO : 0008610, P < 0.001) and regulation of apoptotic process (GO : 0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO : 0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated 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 down-regulated genes for 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 used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.

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“…Smelt is an anadromous species (Saruwatari, Lopez, & Pietsch, 1997), however, now it is cultivated in many reservoirs in South Korea. In a previous study, smelt samples from South Korea were identified as H. nipponensis (Choi & Kim, 2019).…”

Section: Introductionmentioning

confidence: 99%

Draft Genome of the Korean smeltHypomesus nipponensisand its transcriptomic responses to heat stress in the liver and muscle

Xuan

Park

Choi

et al. 2021

Preprint

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Backgrounds: Hypomesus nipponensis is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming. Aim of the study: Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. Methods: 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) versus warm (HT, 23°C) conditions, to identify heat stress-induced genes and gene categories. Results: We observed a total of 1,987 contigs, with N50 of 0.46 Gbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KO (KEGG Orthology). In the missing and gained genes analysis, we detected 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes with coverage less than 10% and for gained genes found from alignment to other species that human, zebrafish and salmon, respectively, we observed 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes with coverage less than 10% compared with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs, adjusted p-value < 0.05) were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated 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 down-regulated genes for nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. Conclusion: The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and be useful for better survival of the smelt and its closely related species under global warming.

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Complete mitochondrial genome sequence and SNPs of the Korean smeltHypomesus nipponensis(Osmeriformes, Osmeridae)

Cited by 4 publications

References 6 publications

Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt

Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt

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

Draft Genome of the Korean smeltHypomesus nipponensisand its transcriptomic responses to heat stress in the liver and muscle

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