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Transcriptome Studies of Salmonid Fishes of the Genius Oncorhynchus

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Abstract

The review is devoted to the current state of research on salmonid fishes in natural populations and aquaculture, performed using high-throughput transcriptomics technologies. The studies describing the molecular basis of fish growth and development, as well as studies on genetic variation underlying the ecological and evolutionary adaptations of the genus Oncorhynchus, are evaluated. Systemic changes in small, long, and circular noncoding RNAs profiles that occur in fish transcriptomes in response to different effects are characterized. The identified signaling cascades, which play key roles in the development of economically valuable traits, can be used as targets for selective fish breeding within the framework of targeted commercial traits.

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REFERENCES

  1. Rao, M.S., Van Vleet, T.R., and Ciurlionis, R., et al., Comparison of RNA-seq and microarray gene expression platforms for the toxicogenomic evaluation of liver from short-term rat toxicity studies, Front Genet., 2019, vol. 9, article 636. https://doi.org/10.3389/fgene.2018.00636

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Thorpe, J.E. and Metcalfe, N.B., Is smolting a positive or a negative developmental decision?, Aquaculture, 1998, vol. 168, pp. 95—103.

    Article  Google Scholar 

  3. Hoar, W.S., Smolt transformation—evolution, behavior, and physiology, J. Fish. Res. Can., 1976, vol. 33, pp. 1233—1252.

    Article  Google Scholar 

  4. Dickhoff, W.W., Beckman, B.R., Larsen, D.A., et al., The role of growth in endocrine regulation of salmon smoltification, Fish Physiol. Biochem., 1997, vol. 17, pp. 231—236. https://doi.org/10.1023/A:1007710308765

    Article  CAS  Google Scholar 

  5. Dodson, J.J., Aubin-Horth, N., Theriault, V., and Paez, D.J., The evolutionary ecology of alternative migratory tactics in salmonid fishes, Biol. Reviews, 2013, vol. 88, pp. 602—625. https://doi.org/10.1111/brv.12019

    Article  Google Scholar 

  6. Folmar, L.C. and Dickhoff, W.W., The parr-smolt transformation (smoltification) and seawater adaptation in salmonids—a review of selected literature, Aquaculture, 1980, vol. 21, pp. 1—37. https://doi.org/10.1016/0044-8486(80)90123-4

    Article  CAS  Google Scholar 

  7. Stefansson, S.O., Bjornsson, B.T., Ebbesson, L.O.E., and McCormick, S.D., Smoltification, in Fish Larval Physiology, Enfield NH: Science, 2008, pp. 639—681.

    Google Scholar 

  8. McCormick, S.D., Smolt physiology and endocrinology, in Euryhaline Fishes, Oxford, 2013, pp. 199—251. https://doi.org/10.1016/B978-0-12-396951-4.00005-0

  9. Lee, S.Y., Lee, H.J., and Kim, Y.K., Comparative transcriptome profiling of selected osmotic regulatory proteins in the gill during seawater acclimation of chum salmon (Oncorhynchus keta) fry, Sci. Rep., 2020, vol. 10, I. 1, article 1987. https://doi.org/10.1038/s41598-020-58915-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Houde, L.A.S., Schulze, A.D., Kaukinen, K.H., et al., Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments, Comp. Biochem. Physiol., D: Genomics Proteomics, 2019, vol. 29, pp. 32—42. https://doi.org/10.1016/j.cbd.2018.10.002

    Article  CAS  PubMed  Google Scholar 

  11. Jeffries, K.M., Hinch, S.G., Gale, M.K., et al., Immune response genes and pathogen presence predict migration survival in wild salmon smolts, Mol. Ecol., 2014, vol. 23, no. 23, pp. 5803—5815. https://doi.org/10.1111/mec.12980

    Article  CAS  PubMed  Google Scholar 

  12. Danzmann, R.G., Kocmarek, A.L., Norman, J.D., et al., Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients, BMC Genomics, 2016, vol. 17, article 60. https://doi.org/10.1186/s12864-016-2363-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hale, M.C., McKinney, G.J., Thrower, F.P., and Nichols, K.M., RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss), Comp. Biochem. Physiol., D: Genomics Proteomics, 2016, vol. 20, pp. 136—150. https://doi.org/10.1016/j.cbd.2016.07.006

    Article  CAS  PubMed  Google Scholar 

  14. Pankhurst, N.W., Ludke, S.L., King, H.R., and Peter, R.E., The relationship between acute stress, food intake, endocrine status and life history stage in juvenile farmed Atlantic salmon, Salmo salar, Aquaculture, 2008, vol. 275, pp. 311—318. https://doi.org/10.1016/j.aquaculture.2008.01.001

    Article  CAS  Google Scholar 

  15. McCormick, S.D., Hansen, L.P., Quinn, T.P., and Saunders, R.L., Movement, migration, and smolting of Atlantic salmon (Salmo salar), Can. J. Fish. Aquat. Sci., 1998, vol. 55, pp. 77—92. https://doi.org/10.1139/d98-011

    Article  Google Scholar 

  16. Jørgensen, E.H., Martinsen, M., Strom, V., et al., Long-term fasting in the anadromous Arctic charr is associated with downregulation of metabolic enzyme activity and upregulation of leptin A1 and SOCS expression in the liver, J. Exp. Biol., 2013, vol. 216, pp. 3222—3230. https://doi.org/10.1242/jeb.088344

    Article  CAS  PubMed  Google Scholar 

  17. Palstra, A.P., Fukaya, K., Chiba, H., et al., The olfactory transcriptome and progression of sexual maturation in homing chum salmon Oncorhynchus keta, PLoS One, 2015, vol. 10, no. 9. e0137404. https://doi.org/10.1371/journal.pone.0137404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Prince, D.J., O’Rourke, S.M., Thompson, T.Q., et al., The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation, Sci. Adv., 2017, vol. 3, e1603198. https://doi.org/10.1126/sciadv.1603198

    Article  PubMed  PubMed Central  Google Scholar 

  19. Crête-Lafrenière, A., Weir, L.K., and Bernatchez, L., Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling, PLoS One, 2012, vol. 7, e46662. https://doi.org/10.1371/journal.pone.0046662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Zhivotovsky, L.A., Genetic history of salmonid fishes of the genus Oncorhynchus, Russ. J. Genet., 2015, vol. 51, no.5, pp. 491—505. https://doi.org/10.1134/S1022795415050105

    Article  CAS  Google Scholar 

  21. Hecht, B.C., Matala, A.P., Hess, J.E., and Narum, S.R., Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range, Mol. Ecol., 2015, vol. 24, pp. 5573—5595. https://doi.org/10.1111/mec.13409

    Article  PubMed  Google Scholar 

  22. Narum, S.R., Di Genova, A., Micheletti, S.J., and Maass, A., Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon, Proc. Biol. Sci., 2018, vol. 285, no. 1883, article 20180935. https://doi.org/10.1098/rspb.2018.0935

  23. Mi, H., Huang, X., Muruganujan, A., et al., PANTHER version 11: expanded annotation data from Gene Ontology and reactome pathways, and data analysis tool enhancements, Nucleic Acids Res., 2016, vol. 45, pp. D183—D189. https://doi.org/10.1093/nar/gkw1138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Evans, T.G., Hammill, E., Kaukinen, K., et al., Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration, Mol. Ecol., 2011, vol. 20, no. 21, pp. 4472—4489. https://doi.org/10.1111/j.1365-294X.2011.05276.x

    Article  CAS  PubMed  Google Scholar 

  25. Madaro, A., Torrissen, O., Whatmore, P., et al., Red and White Chinook salmon (Oncorhynchus tshawytscha): differences in the transcriptome profile of muscle, liver, and pylorus, Mar. Biotechnol. (New York), 2020, vol. 22, no. 4, pp. 581—593. https://doi.org/10.1007/s10126-020-09980-5

  26. Hu, G., Gu, W., Sun, P., et al., Transcriptome analyses reveal lipid metabolic process in liver related to the difference of carcass fat content in rainbow trout (Oncorhynchus mykiss), Int. J. Genomics, 2016, vol. 2016, article 7281585. https://doi.org/10.1155/2016/7281585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Al-Tobasei, R., Ali, A., Leeds, T.D., et al., Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout, BMC Genomics, 2017, vol. 18, article 582. https://doi.org/10.1186/s12864-017-3992-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Paneru, B.D., Tobasei, R.A., Kenney, B., et al., RNA-Seq reveals microRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout, Sci. Rep., 2017, vol. 7, article 9078. https://doi.org/10.1038/s41598-017-09515-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Salem, M., Vallejo, R.L., Leeds, T.D., et al., RNA-seq identifies SNP markers for growth traits in rainbow trout, PLoS One, 2012, vol. 7, no. 5, e36264. https://doi.org/10.1371/journal.pone.0036264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Haard, N.F., Control of chemical composition and food quality attributes of cultured fish, Food Res., 1992, no. 25, pp. 289—307. https://doi.org/10.1016/0963-9969(92)90126-P

  31. Lie, Ø., Flesh quality—the role of nutrition, Aquaculture, 2001, vol. 32, pp. 341—348. https://doi.org/10.1046/j.1355-557x.2001.00026.x

    Article  Google Scholar 

  32. Palstra, A.P. and Planas, J.V., Fish under exercise, Fish Physiol. Biochem., 2011, vol. 37, pp. 259—272. https://doi.org/10.1007/s10695-011-9505-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Magnoni, L.J., Crespo, D., Ibarz, A., et al., Effects of sustained swimming on the red and white muscle transcriptome of rainbow trout (Oncorhynchus mykiss) fed a carbohydrate-rich diet, Comp. Biochem. Physiol., A: Mol. Integr. Physiol., 2013, vol. 166, no. 3, pp. 510—521. https://doi.org/10.1016/j.cbpa.2013.08.005

    Article  CAS  Google Scholar 

  34. Lazzarotto, V., Médale, F., Larroquet, L., and Corraze, G., Long-term dietary replacement of fishmeal and fish oil in diets for rainbow trout (Oncorhynchus mykiss): effects on growth, whole body fatty acids and intestinal and hepatic gene expression, PLoS One, 2018, vol. 13, no. 1, e0190730. https://doi.org/10.1371/journal.pone.0190730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Callet, T., Dupont-Nivet, M., Cluzeaud, M., et al., Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry, PLoS One, 2018, vol. 13, no. 7, e0201462. https://doi.org/10.1371/journal.pone.0201462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Callet, T., Dupont-Nivet, M., Danion, M., et al., Why do some rainbow trout genotypes grow better with a complete plant-based diet? Transcriptomic and physiological analyses on three isogenic lines, Front. Physiol., 2021, vol. 12, article 732321. https://doi.org/10.3389/fphys.2021.732321

    Article  PubMed  PubMed Central  Google Scholar 

  37. Le Boucher, R., Dupont-Nivet, M., Vandeputte, M., et al., Selection for adaptation to dietary shifts: towards sustainable breeding of carnivorous fish, PLoS One, 2012, vol. 7, e44898. https://doi.org/10.1371/journal.pone.0044898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Callet, T., Médale, F., Larroquet, L., et al., Successful selection of rainbow trout (Oncorhynchus mykiss) on their ability to grow with a diet completely devoid of fish meal and fish oil, and correlated changes in nutritional traits, PLoS One, 2017, vol. 12, e0186705. https://doi.org/10.1371/journal.pone.0186705

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Pacitti, D., Lawan, M.M., Feldmann, J., et al., Impact of selenium supplementation on fish antiviral responses: a whole transcriptomic analysis in rainbow trout (Oncorhynchus mykiss) fed supranutritional levels of Sel-Plex®, BMC Genomics, 2016, vol. 17, article 116. https://doi.org/10.1186/s12864-016-2418-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Ma, H., Weber, G.M., Hostuttler, M.A., et al., MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout (Oncorhynchus mykiss), BMC Genomics, 2015, vol. 16, I. 1, article 201. https://doi.org/10.1186/s12864-015-1400-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ma, H., Martin, K., Dixon, 2nd D., et al., Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss, BMC Genomics, 2019, vol. 20, I. 1, article 319. https://doi.org/10.1186/s12864-019-5690-5

    Article  PubMed  PubMed Central  Google Scholar 

  42. Xu, P., McIntyre, L.M., Scardina, J., et al., Transcriptome profiling of embryonic development rate in rainbow trout advanced backcross introgression lines, Mar. Biotechnol. (New York), 2011, vol. 13, no. 2, pp. 215—231. https://doi.org/10.1007/s10126-010-9283-1

    Article  CAS  Google Scholar 

  43. Rebl, A., Korytář, T., Borchel, A., et al., The synergistic interaction of thermal stress coupled with overstocking strongly modulates the transcriptomic activity and immune capacity of rainbow trout (Oncorhynchus mykiss), Sci. Rep., 2020, vol. 10, no. 1, e14913. https://doi.org/10.1038/s41598-020-71852-8

    Article  CAS  Google Scholar 

  44. Jeffries, K.M., Hinch, S.G., Sierocinski, T., et al., Transcriptomic responses to high water temperature in two species of Pacific salmon, Evol. Appl., 2014, vol. 7, no. 2, pp. 286—300. https://doi.org/10.1111/eva.12119

    Article  CAS  PubMed  Google Scholar 

  45. Bowen, L., von Biela, V.R., McCormick, S.D., et al., Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon (Oncorhynchus tshawytscha), Conserv. Physiol., 2020, vol. 8, no. 1, article coaa084. https://doi.org/10.1093/conphys/coaa084

    Article  PubMed  PubMed Central  Google Scholar 

  46. Defo, M.A., Gendron, A.D., Head, J., et al., Cumulative effects of cadmium and natural stressors (temperature and parasite infection) on molecular and biochemical responses of juvenile rainbow trout, Aquat. Toxicol., 2019, vol. 217, article 105347. https://doi.org/10.1016/j.aquatox.2019.105347

    Article  CAS  PubMed  Google Scholar 

  47. Huang, J., Li, Y., Liu, Z., et al., Transcriptomic responses to heat stress in rainbow trout Oncorhynchus mykiss head kidney, Fish Shellfish Immunol., 2018, vol. 82, pp. 32—40. https://doi.org/10.1016/j.fsi.2018.08.002

    Article  CAS  PubMed  Google Scholar 

  48. Rebl, A., Verleih, M., Köbis, J.M., et al., Transcriptome profiling of gill tissue in regionally bred and globally farmed rainbow trout strains reveals different strategies for coping with thermal stress, Mar. Biotechnol. (New York), 2013, vol. 15, no. 4, pp. 445—460. https://doi.org/10.1007/s10126-013-9501-8

    Article  CAS  Google Scholar 

  49. Roh, H., Kim, A., Kim, N., et al., Multi-omics analysis provides novel insight into immuno-physiological pathways and development of thermal resistance in rainbow trout exposed to acute thermal stress, Int. J. Mol. Sci., 2020, vol. 21, no. 23., article 9198. https://doi.org/10.3390/ijms21239198

    Article  CAS  PubMed Central  Google Scholar 

  50. Jeffries, K.M., Hinch, S.G., Sierocinski, T., et al., Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka), Ecol. Evol., 2012, vol. 2, no. 7, pp. 1747—1764. https://doi.org/10.1002/ece3.274

    Article  PubMed  PubMed Central  Google Scholar 

  51. Sutherland, B.J., Jantzen, S.G., Sanderson, D.S., et al., Differentiating size-dependent responses of juvenile pink salmon (Oncorhynchus gorbuscha) to sea lice (Lepeophtheirus salmonis) infections, Comp. Biochem. Physiol., D: Genomics Proteomics, 2011, vol. 6, no. 2, pp. 213—223. https://doi.org/10.1016/j.cbd.2011.04.001

    Article  CAS  PubMed  Google Scholar 

  52. Braden, L.M., Barker, D.E., Koop, B.F., and Jones, S.R., Comparative defense-associated responses in salmon skin elicited by the ectoparasite Lepeophtheirus salmonis, Comp. Biochem. Physiol., D: Genomics Proteomics, 2012, vol. 7, no. 2, pp. 100—109. https://doi.org/10.1016/j.cbd.2011.12.002v

    Article  CAS  PubMed  Google Scholar 

  53. Sutherland, B.J., Koczka, K.W., Yasuike, M., et al., Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis, BMC Genomics, 2014, vol. 15, no. 1, article 200. https://doi.org/10.1186/1471-2164-15-200

    Article  PubMed  PubMed Central  Google Scholar 

  54. Valenzuela-Muñoz, V., Boltaña, S., and Gallardo-Escárate, C., Comparative immunity of Salmo salar and Oncorhynchus kisutch during infestation with the sea louse Caligus rogercresseyi: an enrichment transcriptome analysis, Fish Shellfish Immunol., 2016, vol. 59, pp. 276—287. https://doi.org/10.1016/j.fsi.2016.10.046

    Article  CAS  PubMed  Google Scholar 

  55. Barrett, D.E. and Bartholomew, J.L., A tale of two fish: comparative transcriptomics of resistant and susceptible steelhead following exposure to Ceratonova shasta highlights differences in parasite recognition, PLoS One, 2021, vol. 16, no. 2, e0234837. https://doi.org/10.1371/journal.pone.0234837

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Barrett, D.E., Estensoro, I., Sitjà-Bobadilla, A., and Bartholomew, J.L., Intestinal transcriptomic and histologic profiling reveals tissue repair mechanisms underlying resistance to the parasite Ceratonova shasta, Pathogens, 2021, vol. 10, no. 9, article 1179. https://doi.org/10.3390/pathogens10091179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Rebl, A., Korytář, T., Köbis, J.M., et al., Transcriptome profiling reveals insight into distinct immune responses to Aeromonas salmonicida in gill of two rainbow trout strains, Mar. Biotechnol. (New York), 2014, vol. 16, no. 3, pp. 333—348. https://doi.org/10.1007/s10126-013-9552-x

    Article  CAS  Google Scholar 

  58. Ji, L., Sun, G., Li, X., and Liu, Y., Comparative transcriptome analysis reveals the mechanism of β-glucan in protecting rainbow trout (Oncorhynchus mykiss) from Aeromonas salmonicida infection, Fish Shellfish Immunol., 2020, vol. 98, pp. 87—99. https://doi.org/10.1016/j.fsi.2019.12.022

    Article  CAS  PubMed  Google Scholar 

  59. Rivas-Aravena, A., Fuentes-Valenzuela, M., Escobar-Aguirre, S., et al., Transcriptomic response of rainbow trout (Oncorhynchus mykiss) skeletal muscle to Flavobacterium psychrophilum, Comp. Biochem. Physiol., D: Genomics Proteomics, 2019, vol. 31, article 100596. https://doi.org/10.1016/j.cbd.2019.100596

    Article  CAS  PubMed  Google Scholar 

  60. Wang, D., Sun, S., Li, S., et al., Transcriptome profiling of immune response to Yersinia ruckeri in spleen of rainbow trout (Oncorhynchus mykiss), BMC Genomics, 2021, vol. 22, no. 1, article 292. https://doi.org/10.1186/s12864-021-07611-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Syahputra, K., Kania, P.W., Al-Jubury, A., et al., Transcriptomic analysis of immunity in rainbow trout (Oncorhynchus mykiss) gills infected by Ichthyophthirius multifiliis, Fish Shellfish Immunol., 2019, vol. 86, pp. 486—496. https://doi.org/10.1016/j.fsi.2018.11.075

    Article  CAS  PubMed  Google Scholar 

  62. Zhang, X., Ding, L., Yu, Y., et al., The change of teleost skin commensal microbiota is associated with skin mucosal transcriptomic responses during parasitic infection by Ichthyophthirius multifillis, Front. Immunol., 2018, vol. 9, article 2972. https://doi.org/10.3389/fimmu.2018.02972

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Magnuson, J.T., Cryder, Z., Andrzejczyk, N.E., et al., Metabolomic profiles in the brains of juvenile steelhead (Oncorhynchus mykiss) following bifenthrin treatment, Environ. Sci. Technol., 2020, vol. 54, no. 19, pp. 12245—12253. https://doi.org/10.1021/acs.est.0c04847

    Article  CAS  PubMed  Google Scholar 

  64. Magnuson, J.T., Giroux, M., Cryder, Z., et al., The use of non-targeted metabolomics to assess the toxicity of bifenthrin to juvenile Chinook salmon (Oncorhynchus tshawytscha), Aquat. Toxicol., 2020, vol. 224, article 105518. https://doi.org/10.1016/j.aquatox.2020.105518

    Article  CAS  PubMed  Google Scholar 

  65. Magnuson, J.T., Huff Hartz, K.E., Fulton, C.A., et al., Transcriptomic and histopathological effects of bifenthrin to the brain of juvenile rainbow trout (Oncorhynchus mykiss), Toxics, 2021, vol. 9, no. 3, article 48. https://doi.org/10.3390/toxics9030048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Vehniäinen, E.R., Bremer, K., Scott, J.A., et al., Retene causes multifunctional transcriptomic changes in the heart of rainbow trout (Oncorhynchus mykiss) embryos, Environ. Toxicol. Pharmacol., 2016, vol. 41, pp. 95—102. https://doi.org/10.1016/j.etap.2015.11.015

    Article  CAS  PubMed  Google Scholar 

  67. Rigaud, C., Eriksson, A., Krasnov, A., et al., Retene, pyrene and phenanthrene cause distinct molecular-level changes in the cardiac tissue of rainbow trout (Oncorhynchus mykiss) larvae. Part 1—transcriptomics, Sci. Total Environ., 2020, vol. 745, article 141031. https://doi.org/10.1016/j.scitotenv.2020.141031

    Article  CAS  PubMed  Google Scholar 

  68. Sadoul, B., Birceanu, O., Aluru, N., et al., Bisphenol A in eggs causes development-specific liver molecular reprogramming in two generations of rainbow trout, Sci. Rep., 2017, vol. 7, no. 1, article 14131. https://doi.org/10.1038/s41598-017-13301-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Osachoff, H.L., Brown, L.L.Y., Tirrul, L., et al., Time course of hepatic gene expression and plasma vitellogenin protein concentrations in estrone-exposed juvenile rainbow trout (Oncorhynchus mykiss), Comp. Biochem. Physiol., D: Genomics Proteomics, 2016, vol. 19, pp. 112—119. https://doi.org/10.1016/j.cbd.2016.02.002

    Article  CAS  PubMed  Google Scholar 

  70. Harding, L.B., Schultz, I.R., Goetz, G.W., et al., High-throughput sequencing and pathway analysis reveal alteration of the pituitary transcriptome by 17α-ethynylestradiol (EE2) in female coho salmon, Oncorhynchus kisutch, Aquat. Toxicol., 2013, vols. 142—143, pp. 146—163. https://doi.org/10.1016/j.aquatox.2013.07.020

    Article  CAS  PubMed  Google Scholar 

  71. Détrée, C. and Gonçalves, A.T., Transcriptome mining of apoptotic mechanisms in response to density and functional diets in Oncorhynchus mykiss and role in homeostatic regulation, Comp. Biochem. Physiol., D: Genomics Proteomics, 2019, vol. 31, article 100595. https://doi.org/10.1016/j.cbd.2019.100595

    Article  CAS  PubMed  Google Scholar 

  72. Juanchich, A., Bardou, P., Rué, O., et al., Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing, BMC Genomics, 2016, vol. 17, article 164. https://doi.org/10.1186/s12864-016-2505-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Jarroux, J., Morillon, A., and Pinskaya, M., History, discovery, and classification of lncRNAs, Adv. Exp. Med. Biol., 2017, vol. 1008, pp. 1—46. https://doi.org/10.1007/978-981-10-5203-3_1

    Article  CAS  PubMed  Google Scholar 

  74. Leiva, F., Rojas-Herrera, M., Reyes, D., et al., Identification and characterization of miRNAs and lncRNAs of coho salmon (Oncorhynchus kisutch) in normal immune organs, Genomics, 2020, vol. 112, no. 1, pp. 45—54. https://doi.org/10.1016/j.ygeno.2019.07.015

    Article  CAS  PubMed  Google Scholar 

  75. Giraldez, A.J., Mishima, Y., Rihel, J., et al., Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs, Science, 2006, vol. 312, no. 5770, pp. 75—79. https://doi.org/10.1126/science.1122689

    Article  CAS  PubMed  Google Scholar 

  76. Ma, H., Hostuttler, M., Wei, H., et al., Characterization of the rainbow trout egg microRNA transcriptome, PLoS One, 2012, vol. 7, no. 6, e39649. https://doi.org/10.1371/journal.pone.0039649

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Kostyniuk, D.J., Marandel, L., Jubouri, M., et al., Profiling the rainbow trout hepatic miRNAome under diet-induced hyperglycemia, Physiol. Genomics, 2019, vol. 51, no. 9, pp. 411—431. https://doi.org/10.1152/physiolgenomics.00032.2019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Ma, F., Liu, Z., Huang, J., et al., High-throughput sequencing reveals microRNAs in response to heat stress in the head kidney of rainbow trout (Oncorhynchus mykiss), Funct. Integr. Genomics, 2019, vol. 19, no. 5, pp. 775—786. https://doi.org/10.1007/s10142-019-00682-3

    Article  CAS  PubMed  Google Scholar 

  79. Quan, J., Kang, Y., Luo, Z., et al., Integrated analysis of the responses of a circRNA-miRNA-mRNA ceRNA network to heat stress in rainbow trout (Oncorhynchus mykiss) liver, BMC Genomics, 2021, vol. 22, no. 1, article no. 48. https://doi.org/10.1186/s12864-020-07335-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Cao, Y., Wang, D., Li, S., et al., A transcriptome analysis focusing on splenic immune-related mciroRNAs of rainbow trout upon Aeromonas salmonicida subsp. salmonicida infection, Fish Shellfish Immunol., 2019, vol. 91, pp. 350—357. https://doi.org/10.1016/j.fsi.2019.05.048

    Article  CAS  PubMed  Google Scholar 

  81. Marchese, F.P., Raimondi, I., and Huarte, M., The multidimensional mechanisms of long noncoding RNA function, Genome Biol., 2017, vol. 18, article 206. https://doi.org/10.1186/s13059-017-1348-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Wang, J., Fu, L., Koganti, P.P., et al., Identification and functional prediction of large intergenic noncoding RNAs (lincRNAs) in rainbow trout (Oncorhynchus mykiss), Mar. Biotechnol. (New York), 2016, vol. 18, no. 2, pp. 271—282. https://doi.org/10.1007/s10126-016-9689-5

    Article  CAS  Google Scholar 

  83. Quan, J., Kang, Y., Luo, Z., et al., Identification and characterization of long noncoding RNAs provide insight into the regulation of gene expression in response to heat stress in rainbow trout (Oncorhynchus mykiss), Comp. Biochem. Physiol., D: Genomics Proteomics, 2020, vol. 36, article 100707. https://doi.org/10.1016/j.cbd.2020.100707

    Article  CAS  PubMed  Google Scholar 

  84. Gonçalves, A.T., Núñez-Acuña, G., Détrée, C., and Gallardo-Escárate, C., Coding/non-coding cross-talk in intestinal epithelium transcriptome gives insights on how fish respond to stocking density, Comp. Biochem. Physiol., D: Genomics Proteomics, 2019, vol. 29, pp. 14—23. https://doi.org/10.1016/j.cbd.2018.10.005

    Article  CAS  PubMed  Google Scholar 

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Funding

This study was supported by the Russian Science Foundation (grant no. 19-16-00101; research manager, L.A. Zhivotovsky).

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  1. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia

    A. D. Zolotarenko & M. V. Shitova

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  1. A. D. Zolotarenko
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  2. M. V. Shitova
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Correspondence to M. V. Shitova.

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The authors declare that they have no conflicts of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Translated by N. Maleeva

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Zolotarenko, A.D., Shitova, M.V. Transcriptome Studies of Salmonid Fishes of the Genius Oncorhynchus. Russ J Genet 58, 757–772 (2022). https://doi.org/10.1134/S102279542207016X

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