{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T09:07:10Z","timestamp":1789549630772,"version":"build-2803163510"},"reference-count":33,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100015308","name":"Key Research and Development Projects of the Xinjiang Uygur Autonomous Region","doi-asserted-by":"publisher","award":["2023B02037-2-2"],"award-info":[{"award-number":["2023B02037-2-2"]}],"id":[{"id":"10.13039\/501100015308","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The increasing salinization and alkalization of inland waters in China pose a growing threat to the early developmental stages of fish. This study investigated the survival rates and transcriptomic response mechanisms of pond smelt (Hypomesus nipponensis) embryos, a species naturally adapted to brackish water, under different salinity stresses. Fertilized eggs were exposed to four salinity gradients: freshwater (0\u2030, experimental control) and 7\u2030, 14\u2030, and 21\u2030 for 7 days. The results showed that the upper salinity tolerance limit for embryos was between 21\u2030 and 28\u2030; hatching rates were zero in the 28\u2030 and 35\u2030 groups, and the hatching rate in the 21\u2030 group decreased to 40.3 \u00b1 6.1%. Transcriptome sequencing analysis of the 0\u2030, 7\u2030, 14\u2030, and 21\u2030 groups revealed that salinity stress induced extensive differential gene expression in a non-monotonic response pattern. In the 7\u2030 and 14\u2030 groups, the number of downregulated genes (approximately 10,000) was significantly higher than that of upregulated genes (approximately 3300). In contrast, in the high-salinity 21\u2030 group, upregulated genes increased to 4535. Functional enrichment analysis revealed that the calcium signaling pathway, axon guidance, and glutamatergic synapse pathway were significantly enriched across all salinity groups. Changes in the expression of key differential genes (e.g., sparc, hspa4a, aldob, and csmd1a) further confirmed molecular events such as dysregulation of calcium homeostasis, stress protein activation, metabolic inhibition, and neurodevelopmental regulation. The qRT-PCR validation results were highly consistent with the transcriptome data. This study is the first to systematically reveal the molecular regulatory network of pond smelt embryos in response to increasing salinity relative to a freshwater reference point. Our findings indicate their potential for proliferation in moderate saline\u2013alkaline waters (\u226414\u2030), while high salinity (\u226521\u2030) significantly reduces hatching success and triggers a strong stress response. These results provide an important molecular basis and theoretical reference for the enhancement and aquaculture of this species in saline\u2013alkaline waters.<\/jats:p>","DOI":"10.3390\/ani16182910","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T07:58:59Z","timestamp":1789545539000},"page":"2910","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptome-Based Analysis of the Effects of Salt Stress on the Embryos of Hypomesus nipponensis"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-2636-7220","authenticated-orcid":false,"given":"Qian","family":"Xiao","sequence":"first","affiliation":[{"name":"College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organisms, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"College of Modern Fishery Industry, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Characteristic Aquatic Research Center, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Xinnan","family":"Fu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment 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China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-7566-4142","authenticated-orcid":false,"given":"Zhelan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organisms, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"College of Modern Fishery Industry, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Characteristic Aquatic Research Center, Urumqi 830052, 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Bosteng Lake Ecological Fisheries Co., Ltd., Bohu 841400, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Junjie","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organisms, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"College of Modern Fishery Industry, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Characteristic Aquatic Research Center, Urumqi 830052, 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Jpn. Soc. Fish. Oceanogr."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"jkab147","DOI":"10.1093\/g3journal\/jkab147","article-title":"Draft Genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle","volume":"11","author":"Biao","year":"2021","journal-title":"G3"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Jian, X., Peifeng, J., Baosen, W., Lan, Z., Jian, W., Zixia, Z., Yan, Z., Jiongtang, L., Peng, X., and Xiaowen, S. (2013). Transcriptome sequencing and analysis of wild Amur Ide (Leuciscus waleckii) inhabiting an extreme alkaline-saline lake reveals insights into stress adaptation. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0059703"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Jian, X., Qiang, L., Liming, X., Shaolin, W., Yanliang, J., Zixia, Z., Yan, Z., Jiongtang, L., Chuanju, D., and Peng, X. (2013). Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-682"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Norman, J.D., Robinson, M., Glebe, B., Ferguson, M.M., and Danzmann, R.G. (2012). Genomic arrangement of salinity tolerance QTLs in salmonids: A comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss). BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-420"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1002\/jez.2350","article-title":"The cellular stress response in fish exposed to salinity fluctuations","volume":"333","author":"Evans","year":"2020","journal-title":"J. Exp. Zool. Part A Ecol. Integr. Physiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.aquaculture.2011.12.034","article-title":"Influence of salinity on embryogenesis, survival, growth and oxygen consumption in embryos and yolk-sac larvae of the Nile tilapia","volume":"334\u2013337","author":"Fridman","year":"2012","journal-title":"Aquaculture"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"741883","DOI":"10.1016\/j.aquaculture.2024.741883","article-title":"Integration of transcriptome, histopathology, and physiological indicators reveals regulatory mechanisms of largemouth bass (Micropterus salmoides) in response to carbonate alkalinity stress","volume":"596","author":"Hua","year":"2025","journal-title":"Aquaculture"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"741143","DOI":"10.1016\/j.aquaculture.2024.741143","article-title":"Effects of saline and alkaline stresses on the survival, growth, and physiological responses in juvenile mandarin fish (Siniperca chuatsi)","volume":"591","author":"Li","year":"2024","journal-title":"Aquaculture"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s10499-025-02009-5","article-title":"Changes in the physiological indicators and gene expression for grass carp (Ctenopharyngodon idella) in response to alkaline stress","volume":"33","author":"Chen","year":"2025","journal-title":"Aquac. Int."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"22224","DOI":"10.1038\/s41598-025-96808-8","article-title":"Effects of alkali stress on antioxidant capacity, lipid metabolism, apoptosis and autophagy of Eriocheir sinensis","volume":"15","author":"Liu","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"738964.","DOI":"10.1016\/j.aquaculture.2022.738964","article-title":"Effects of low salinities on growth, fatty acid composition, and transcriptome in Florida pompano (Trachinotus carolinus) at early developmental stages","volume":"563","author":"Bradshaw","year":"2023","journal-title":"Aquaculture"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1186\/s12864-025-12054-2","article-title":"Morphology, transcriptome and physiology analyses reveal adaptation mechanisms of Gymnocypris Przewalskii juveniles to saline-alkaline stresses","volume":"26","author":"Gao","year":"2025","journal-title":"BMC Genom."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1007\/s10126-023-10228-1","article-title":"Histological, Physiological and Transcriptomic Analysis Reveal the Acute Alkalinity Stress of the Gill and Hepatopancreas of Litopenaeus vannamei","volume":"25","author":"Ruiqi","year":"2023","journal-title":"Mar. Biotechnol."},{"key":"ref_15","first-page":"100651","article-title":"Transcriptome changes for Nile tilapia (Oreochromis niloticus) in response to alkalinity stress","volume":"33","author":"Zhao","year":"2020","journal-title":"Comp. Biochem. Physiol. Part D Genom. Proteom."},{"key":"ref_16","first-page":"491","article-title":"Transcriptome and expression profiling analysis of Leuciscus waleckii: An exploration of the alkali-adapted mechanisms of a freshwater teleost","volume":"10","author":"Ran","year":"2014","journal-title":"Mol. Biosyst."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Supplementary methods for the paper transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: New perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Minoru","year":"2017","journal-title":"Nucl. Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1093\/nar\/29.9.e45","article-title":"A new mathematical model for relative quantification in real-time RT-PCR","volume":"29","author":"Pfaffl","year":"2001","journal-title":"Nucl. Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1152\/physiolgenomics.00001.2015","article-title":"Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax)","volume":"47","author":"Kaitetzidou","year":"2015","journal-title":"Physiol. Genom."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"124400","DOI":"10.1016\/j.envpol.2024.124400","article-title":"Unraveling the molecular mechanisms of fish physiological response to freshwater salinization: A comparative multi-tissue transcriptomic study in a river polluted by potash mining","volume":"357","author":"Sierra","year":"2024","journal-title":"Environ. Pollut."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Lai, K.P., Tam, N.Y., Chen, Y., Leung, C.T., Lin, X., Tsang, C.F., Kwok, Y.C., Tse, W.K., Cheng, S.H., and Chan, T.F. (2022). miRNA\u2013mRNA Integrative Analysis Reveals the Roles of miRNAs in Hypoxia-Altered Embryonic Development- and Sex Determination-Related Genes of Medaka Fish. Front. Mar. Sci., 8.","DOI":"10.3389\/fmars.2021.736362"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3015","DOI":"10.1242\/jeb.201.22.3015","article-title":"Evolution of osmotic stress signaling via MAP kinase cascades","volume":"201","author":"Burg","year":"1998","journal-title":"J. Exp. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Isabelle, L., Aur\u00e9lie, L.C., J\u00e9r\u00f4me, M., Sandrine, P., and Alain, F. (2015). Transcriptomic Analysis of Trout Gill Ionocytes in Fresh Water and Sea Water Using Laser Capture Microdissection Combined with Microarray Analysis. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0139938"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1073\/pnas.0408956102","article-title":"Rapid hyperosmotic coinduction of two tilapia (Oreochromis mossambicus) transcription factors in gill cells","volume":"102","author":"Fiol","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"105113","DOI":"10.1016\/j.jprot.2024.105113","article-title":"Quantitative proteomic and metabolomic profiling reveals different osmoregulation mechanisms of tilapia cells coping with different hyperosmotic stress","volume":"296","author":"Pan","year":"2024","journal-title":"J. Proteom."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/s40104-024-01100-w","article-title":"Proline metabolism is essential for alkaline adaptation of Nile tilapia (Oreochromis niloticus)","volume":"15","author":"Wang","year":"2024","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Zhou, L., Ma, Z., Chen, X., Liu, Q., Huang, Y., Yang, C., Zeng, D., Zheng, Z., Zhang, B., and Zhang, Y. (2026). Carbonic Anhydrase 2 and Na+\/K+-ATPase Mediate Family-Dependent Nitrite Tolerance via Modulating Branchial Ion Transport and Acid\u2013Base Balance in Penaeus vannamei. Animals, 16.","DOI":"10.3390\/ani16111638"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Sapozhnikova, Y.P., Koroleva, A.G., Sidorova, T.V., Potapov, S.A., Epifantsev, A.A., Vakhteeva, E.A., Tolstikova, L.I., Glyzina, O.Y., Yakhnenko, V.M., and Cherezova, V.M. (2024). Transcriptional Rearrangements Associated with Thermal Stress and Preadaptation in Baikal Whitefish (Coregonus baicalensis). Animals, 14.","DOI":"10.3390\/ani14213077"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Ding, L., Liu, Y., Wei, X., Geng, C., Liu, W., Han, L., Yuan, F., Wang, P., and Sun, Y. (2023). Effects of saline-alkaline stress on metabolome, biochemical parameters, and histopathology in the kidney of crucian carp (Carassius auratus). Metabolites, 13.","DOI":"10.3390\/metabo13020159"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"110948","DOI":"10.1016\/j.cbpb.2024.110948","article-title":"Alternative splicing patterns of hnrnp genes in gill tissues of rainbow trout (Oncorhynchus mykiss) during salinity changes","volume":"271","author":"Liu","year":"2024","journal-title":"Comp. Biochem. Physiol. Part B"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/s40104-025-01215-8","article-title":"Nutritional strategies for Nile tilapia: Protein and carbohydrate balances in saline-alkaline aquaculture","volume":"16","author":"Liu","year":"2025","journal-title":"J. Anim. Sci. Biotechnol."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2910\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T08:32:22Z","timestamp":1789547542000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2910"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":33,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ani16182910"],"URL":"https:\/\/doi.org\/10.3390\/ani16182910","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]}}}