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Tetraodon (Tetraodon nigroviridis) süperoksit dismutaz genlerinin (sod1, sod2 ve sod3) in siliko analizi ve dokuya özgü gen ekspresyon profili

Year 2024, Volume: 41 Issue: 4, 261 - 272, 11.12.2024

Büşra Kaya , Mehtap Bayır

https://doi.org/10.12714/egejfas.41.4.02

Abstract

Bu araştırmanın amacı, tetraodon (Tetraodon nigroviridis) süperoksit dismutaz (sod1, sod2 ve sod3) genleri üzerinde in siliko analizler yapmak, biyoenformatik araçlar kullanarak bu genlerin çeşitli dokulardaki (bağırsak, beyin, böbrek, karaciğer, kas, kalp, göz, dalak, solungaçlar, mide, yumurtalık ve testis) gen ekspresyonlarını değerlendirmektir. Bu hedefe ulaşmak için, yukarıda belirtilen organlardan cDNA elde etmek amacıyla erkek ve dişi balıklardan doku örnekleri alındı. Her dokudan toplam RNA izole edildi ve ardından sods genlerinin transkriptleri qPCR kullanılarak değerlendirildi. Transkript miktarlarının belirlenmesi amacıya ise RT-qPCR yapıdı. İn siliko analizler, gen yapısının incelenmesini, korunmuş gen sentenisi analizlerini, filogenetik ağaç analizlerini ve diğer omurgalılarla benzerlik-özdeşlik oranlarının tespitini kapsamaktadır. Tetraodon sod1 geninin erkek ve dişi dokularındaki transkripsiyon farklılıkları incelendiğinde, kalp dokusu dışında çalışılan tüm diğer dokularda (karaciğer, bağırsak, kas, beyin, gözler, dalak, solungaçlar, böbrek, mide ve gonadlar dahil) erkek balıklarda anlamlı derecede daha yüksek ekspresyon seviyeleri gözlendi. Erkek ve dişi tetraodonlarda sod2 geninin sonuçları incelendiğinde, karaciğer, kas, solungaçlar, bağırsak, yumurtalık ve testiste anlamlı bir yukarı düzenleme gözlendi; bağırsak, kalp ve gonadlar gibi dokularda ise istatistiksel olarak anlamlı bir fark görülmedi. Erkek ve dişi tetraodonlarda sod3 geni ile ilgili olarak, kalp, dalak ve mide dokuları istatistiksel olarak anlamlılık göstermedi, ancak karaciğer, bağırsak, solungaçlar, böbrek, mide ve gonadlar erkek balıklarda anlamlı derecede daha yüksek ekspresyon sergiledi (p<0.05).

Keywords

Tetraodon in silico analizler sods genleri gen ekspresyonu

Project Number

FYL-2021-9735

References

  • Ahn, H., Lee, C., Nam, B.H., Kim, E.B, Caetano-Anolles, K., & Kim, H. (2018). Selective pressure on the protein-coding genes of the pufferfish is correlated with phenotypic traits. Marine Genomics, 37, 182-186. https://doi.org/10.1016/j.margen.2017.11.015
  • Anderson, K., & Elizur, A. (2012). Hepatic reference gene selection in adult and juvenile female Atlantic salmon at normal and elevated temperatures. BMC Research Notes, 5(21), 1 9. https://doi.org/10.1186/1756-0500-5-21
  • Bayır, M. (2020). In Silico Analysis of Cu-Zn superoxide dismutase and Mn superoxide dismutase genes in fugu (Takifugu rubripes). Pakistan Journal of Zoology, 52(4), 1377 1382. https://doi.org/10.17582/journal.pjz/20190122060142
  • Bayır, M., & Arslan, G. (2020). Bioinformatics analysis of fugu (Fugu rubripes) catalase (cat) Gene. Turkish Journal of Agriculture Food Science and Technology, 8(6), 1413-1417. https://doi.org/10.24925/turjaf.v8i6.1413-1417.3353
  • Bayır, M., & Özdemir, E. (2023). Genomic organization and transcription of superoxide dismutase genes (sod1, sod2, and sod3b) and response to diazinon toxicity in platyfish (Xiphophorus maculatus) by using SOD enzyme activity. Animal Biotechnology, 34(88), 3578-3588. https://doi.org/10.1080/10495398.2023.2178931
  • Böhne, A., Sengstag, T., & Salzburger, W. (2014). Comparative transcriptomics in East African cichlids reveals sex- and species-specific expression and new candidates for sex differentiation in fishes. Genome Biology and Evolution, 6(9), 2567–2585. https://doi.org/10.1093/gbe/evu200
  • Braasch, I., & Postlethwait, J.H.I. (2012). Polyploidy in fish and the teleost genome duplication. In P. S. Soltis & D. E. Soltis (Eds.), Polyploidy and Genome Evolution, 341–383. Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-31442-1_17
  • Carney Almroth, B., Asker, N., Wassmur, B., Rosengren, M., Jutfelt, F., Gräns, A., Sundell, K., Axelsson, M., & Sturve, J. (2015). Warmer water temperature results in oxidative damage in an Antarctic fish, the bald notothen. Journal of Experimental Marine Biology and Ecology, 468, 130-137. https://doi.org/10.1016/j.jembe.2015.04.002
  • Chatzidimitriou, E., Bisaccia, P., Corrà, F., Bonato, M., Irato, P., Manuto, L., Toppo, S., Bakiu, R., & Santovito, G. (2020). Copper/zinc superoxide dismutase from the crocodile icefish Chionodraco hamatus: Antioxidant defense at constant sub-zero temperature. Antioxidants (Basel), 9(4), 325. https://doi.org/10.3390/antiox9040325
  • Chen, C.C., Rodriguez, I.B., Chen, Y.L., Zehr, J. P., Chen, Y.R., Hsu, S.T.D., Yang, S.C., & Ho, T.Y. (2022). Nickel superoxide dismutase protects nitrogen fixation in Trichodesmium. Letters in Organic Chemistry, 7(4), 363-371. https://doi.org/10.1002/lol2.10263
  • Elsevar, B.I., & Bayır, M. (2023). Bioinformatics studies and comparison of mRNA transcription of glutathione S-transferase gene in some tissues of common carp (Cyprinus carpio) and brown trout (Salmo trutta). Ege Journal of Fisheries and Aquatic Sciences, 40(4), 266-275. https://doi.org/10.12714/egejfas.40.4.05
  • Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376. https://doi.org/10.1007/BF01734359
  • Ferrão, L., Blanes-García, M., Pérez, L., Asturiano, J.F., & Morini, M. (2024). Superoxidase dismutases (SODs) in the European eel: Gene characterization, expression response to temperature combined with hormonal maturation and possible migratory implications. Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology, 111590.
  • Fujii, J., Homma, T., & Osaki, T. (2022). Superoxide radicals in the execution of cell death. Antioxidants (Basel),11(3), 501. https://doi.org/10.3390/antiox11030501
  • Glasauer, S.M., & Neuhauss, S.C. (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics, 289(6), 1045-1060. https://doi.org/10.1007/s00438-014-0889-2
  • Grath, S., & Parsch, J. (2016). Sex-biased gene expression. Annual Review of Genetics, 50, 29–44. https://doi.org/10.1146/annurev-genet-120215-035429
  • Guan, G., Kobayashi, T., & Nagahama, Y. (2000). Sexually dimorphic expression of two types of DM (Doublesex/Mab-3)-domain genes in a teleost fish, the Tilapia (Oreochromis niloticus). Biochemical and Biophysical Research Communications, 272(3), 662-6. https://doi.org/10.1006/bbrc.2000.2840
  • Inoue, Y., Suenaga, Y., Yoshiura, Y., Moritomo, T., Ototake, M., & Nakanishi, T. (2004). Molecular cloning and sequencing of Japanese pufferfish (Takifugu rubripes) NADPH oxidase cDNAs. Developmental and Comparative Immunology, 28, 911 925. https://doi.org/10.1016/j.dci.2004.03.002
  • Isensee, J., & Noppinger, P.R. (2007). Sexually dimorphic gene expression in mammalian somatic tissue. Gender Medicine, 4(2), 75-95. https://doi.org/10.1016/S1550-8579(07)80049-0
  • Kim, J.H., Rhee, J.S., Lee, J.S., Dahms, H.U., Lee, J., Han, K.N., & Lee, J.S. (2010). Effect of cadmium exposure on expression of antioxidant gene transcripts in the river pufferfish, Takifugu obscurus (Tetraodontiformes). Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 152(4), 473 9. https://doi.org/10.1016/j.cbpc.2010.08.002
  • Kim, C.H., Kim, E.J., & Nam, Y.K. (2021). Superoxide dismutase multigene family from a primitive chondrostean sturgeon, Acipenser baerii: Molecular characterization, evolution, and antioxidant defense during development and pathogen infection. Antioxidants (Basel), 10(2), 232. https://doi.org/10.3390/antiox10020232
  • Koh, C.G., Oon, S.H., & Brenner, S. (1997). Serine/threonine phosphatases of the pufferfish, Fugu rubripes. Gene, 198(1–2), 223-228. https://doi.org/10.1016/S0378-1119(97)00318-1
  • Koop, B.F., & Nadeau, J.H. (1996). Pufferfish and new paradigm for comparative genome analysis. Proceedings of the National Academy of Sciences of the United States of America, 93(4), 1363-5. https://doi.org/10.1073/pnas.93.4.1363
  • Lee, J.H., Kondo, H., Sato, S., Akimoto, S., Saito, T., Kodama, M., & Watabe, S. (2007). Identification of novel genes related to tetrodotoxin intoxication in pufferfish. Toxicon, 49(7), 939 53. https://doi.org/10.1016/j.toxicon.2007.01.008
  • Matzuk, M.M., Dionne, L., Guo, Q., Kumar, R.T., & Russell, M. (1998). Ovarian function in superoxide dismutase 1 and 2 knockout mice. Endocrinology, 139(9), 4008 4011. https://doi.org/10.1210/endo.139.9.6289
  • Remsen, D. (2016). The use and limits of scientific names in biological informatics. ZooKeys, 207 223. https://doi.org/10.3897/zookeys.550.9546
  • Roest Crollius, H., Jaillon, O., Dasilva, C., Ozouf-Costaz, C., Fizames, C., Fischer, C., Bouneau, L., Billault, A., Quétier, F., Saurin, W., Bernot, A., & Weissenbach, J. (2000). Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Research, 10 7, 939-49. https://doi.org/10.1101/GR.10.7.939
  • Rothenburg, S., Deigendesch, N., Dey, M., Dever T.E. & Tazi, L. (2008). Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: Varying the number of double-stranded RNA binding domains and lineage-specific duplications, BMC Biology, 6, 12 https://doi.org/10.1186/1741-7007-6-12
  • Sheng, Y., Abreu, I.A., Cabelli, D.E., Maroney, M.J., Miller, A.F., Teixeira, M., & Valentine, J.S. (2014). Superoxide dismutases and superoxide reductases. Chemical Reviews, 114, 3854-3918. https://doi.org/10.1021/cr4005296
  • Sheraz, A., Zhu, H., Dong, Q., Wang, T., Zong, S., Wang, H., Ge, L., & Wu, T. (2023). The superoxide dismutase (SOD) genes family mediates the response of Nilaparvata lugens to jinggangmycin and sugar. Frontiers in Physiology, 10(14), 1197395. https://doi.org/10.3389/fphys.2023.1197395
  • Stump, E., Ralph, G.M., Comeros-Raynal, M.T., Matsuura, K., & Carpenter, K.E. (2018). Global conservation status of marine pufferfishes (Tetraodontiformes: Tetraodontidae). Global Ecology and Conservation, 14, e00388. https://doi.org/10.1016/j.gecco.2018.e00388
  • Taşbozan, O., Erbaş, C., Bayır, M., Özdemir, E., & Bayır, A. (2022). Identification, characterization and nutritional regulation of fatty acid-binding protein (fabp) genes by vegetable oils in European seabass (Dicentrarchus labrax) reared in low water temperatures. Aquaculture Research, 53(18), 6683-6699. https://doi.org/10.1111/are.16137
  • Thompson, J.D., Higgins, D.G., & Gibson, T.J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  • Uzun, B.N., & Bayır, M. (2023). Bioinformatics studies and examining the tissue distribution of glutathione reductase and glucose-6-phosphate dehydrogenase genes to investigate gender differences in differences in stress tolerance in zebrafish (Danio rerio). Marine Science and Technology Bulletin, 12(3), 352 369. https://doi.org/10.33714/masteb.1337231
  • Wang, W., Xia, M.X., Chen, J., Yuan, R., Deng, F.N., & Shen, F.F. (2016). Gene expression characteristics and regulation mechanisms of superoxide dismutase and its physiological roles in plants under stress. Biochemistry (Moscow), 81(5), 465 80. https://doi.org/10.1134/S0006297916050047
  • Watson, C.A., Hill, J.E., Graves, J.S., Wood, A.L., & Kilgore, K.H. (2009). Use of a novel induced spawning technique for the first reported captive spawning of Tetraodon nigroviridis. Marine Genomics, 2(2), 143-146. https://doi.org/10.1016/j.margen.2009.04.004

Computational analysis of superoxide dismutase genes (sod1, sod2, and sod3) and comprehensive tissue-specific gene expression profiling in Tetraodon (Tetraodon nigroviridis)

Year 2024, Volume: 41 Issue: 4, 261 - 272, 11.12.2024

Büşra Kaya , Mehtap Bayır

https://doi.org/10.12714/egejfas.41.4.02

Abstract

The objective of this investigation was to conduct in silico analyses on superoxide dismutase (sod1, sod2, and sod3) genes in tetraodon (Tetraodon nigroviridis), employing bioinformatics tools, and to assess the gene expressions in various tissues such as the intestine, brain, kidney, liver, muscle, heart, eye, spleen, gills, stomach, ovary, and testis of tetraodon. To achieve this, tissue samples were obtained from both male and female tetraodon, spanning the aforementioned organs, with the purpose of acquiring cDNA. Total RNA was isolated from each tissue, and subsequently, the transcripts of sods genes were assessed using qPCR, while transcript quantities were determined through RT-qPCR. The in silico analyses encompassed the examination of gene structure, conserved gene synteny, phylogenetic tree analyses, and the identification of similarity-identity ratios with other vertebrates. When examining the transcriptional differences between male and female tissues for the Tetraodon sod1 gene, it was noted that, except for the heart tissue, all other tissues studied (including the liver, intestine, muscle, brain, eyes, spleen, gills, kidney, stomach, and gonads) exhibited significantly higher expression levels in male fish. Examining the results for the sod2 gene in male and female tetraodon, significant upregulation was observed in the liver, muscle, gills, intestine, ovary, and testis, with no statistical significance in tissues like the intestine, heart, and gonads. Regarding the sod3 gene in male and female tetraodon, heart, spleen, and stomach tissues did not show statistical significance, but the liver, intestine, gills, kidney, stomach, and gonads exhibited significantly higher expression in male fish (p<0.05).

Keywords

Tetraodon in silico analyses sods genes gene expression

Ethical Statement

"Balon Balığı (Tetraodon nigroviridis)’nda Süperoksit dismutaz (sod1, sod2, sod3b) Genlerinin nsiliko Analizleri ve Gen Ekspresyonlarnn Tüm Dokularda Belirlenmesi” isimli yüksek lisans tez çalışması ile ilgili Hayvan Deneyleri Yerel Etik Kurulunun 30.07.2021 tarihli ve 6 sayılı oturumunda, 177 nolu kararı ile uygun görüldüğü 02.08.2021 tarih ve 2100198805 sayılı yazı ile bidirilmiştir.

Supporting Institution

Atatürk Üniversitesi

Project Number

FYL-2021-9735

References

  • Ahn, H., Lee, C., Nam, B.H., Kim, E.B, Caetano-Anolles, K., & Kim, H. (2018). Selective pressure on the protein-coding genes of the pufferfish is correlated with phenotypic traits. Marine Genomics, 37, 182-186. https://doi.org/10.1016/j.margen.2017.11.015
  • Anderson, K., & Elizur, A. (2012). Hepatic reference gene selection in adult and juvenile female Atlantic salmon at normal and elevated temperatures. BMC Research Notes, 5(21), 1 9. https://doi.org/10.1186/1756-0500-5-21
  • Bayır, M. (2020). In Silico Analysis of Cu-Zn superoxide dismutase and Mn superoxide dismutase genes in fugu (Takifugu rubripes). Pakistan Journal of Zoology, 52(4), 1377 1382. https://doi.org/10.17582/journal.pjz/20190122060142
  • Bayır, M., & Arslan, G. (2020). Bioinformatics analysis of fugu (Fugu rubripes) catalase (cat) Gene. Turkish Journal of Agriculture Food Science and Technology, 8(6), 1413-1417. https://doi.org/10.24925/turjaf.v8i6.1413-1417.3353
  • Bayır, M., & Özdemir, E. (2023). Genomic organization and transcription of superoxide dismutase genes (sod1, sod2, and sod3b) and response to diazinon toxicity in platyfish (Xiphophorus maculatus) by using SOD enzyme activity. Animal Biotechnology, 34(88), 3578-3588. https://doi.org/10.1080/10495398.2023.2178931
  • Böhne, A., Sengstag, T., & Salzburger, W. (2014). Comparative transcriptomics in East African cichlids reveals sex- and species-specific expression and new candidates for sex differentiation in fishes. Genome Biology and Evolution, 6(9), 2567–2585. https://doi.org/10.1093/gbe/evu200
  • Braasch, I., & Postlethwait, J.H.I. (2012). Polyploidy in fish and the teleost genome duplication. In P. S. Soltis & D. E. Soltis (Eds.), Polyploidy and Genome Evolution, 341–383. Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-31442-1_17
  • Carney Almroth, B., Asker, N., Wassmur, B., Rosengren, M., Jutfelt, F., Gräns, A., Sundell, K., Axelsson, M., & Sturve, J. (2015). Warmer water temperature results in oxidative damage in an Antarctic fish, the bald notothen. Journal of Experimental Marine Biology and Ecology, 468, 130-137. https://doi.org/10.1016/j.jembe.2015.04.002
  • Chatzidimitriou, E., Bisaccia, P., Corrà, F., Bonato, M., Irato, P., Manuto, L., Toppo, S., Bakiu, R., & Santovito, G. (2020). Copper/zinc superoxide dismutase from the crocodile icefish Chionodraco hamatus: Antioxidant defense at constant sub-zero temperature. Antioxidants (Basel), 9(4), 325. https://doi.org/10.3390/antiox9040325
  • Chen, C.C., Rodriguez, I.B., Chen, Y.L., Zehr, J. P., Chen, Y.R., Hsu, S.T.D., Yang, S.C., & Ho, T.Y. (2022). Nickel superoxide dismutase protects nitrogen fixation in Trichodesmium. Letters in Organic Chemistry, 7(4), 363-371. https://doi.org/10.1002/lol2.10263
  • Elsevar, B.I., & Bayır, M. (2023). Bioinformatics studies and comparison of mRNA transcription of glutathione S-transferase gene in some tissues of common carp (Cyprinus carpio) and brown trout (Salmo trutta). Ege Journal of Fisheries and Aquatic Sciences, 40(4), 266-275. https://doi.org/10.12714/egejfas.40.4.05
  • Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376. https://doi.org/10.1007/BF01734359
  • Ferrão, L., Blanes-García, M., Pérez, L., Asturiano, J.F., & Morini, M. (2024). Superoxidase dismutases (SODs) in the European eel: Gene characterization, expression response to temperature combined with hormonal maturation and possible migratory implications. Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology, 111590.
  • Fujii, J., Homma, T., & Osaki, T. (2022). Superoxide radicals in the execution of cell death. Antioxidants (Basel),11(3), 501. https://doi.org/10.3390/antiox11030501
  • Glasauer, S.M., & Neuhauss, S.C. (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics, 289(6), 1045-1060. https://doi.org/10.1007/s00438-014-0889-2
  • Grath, S., & Parsch, J. (2016). Sex-biased gene expression. Annual Review of Genetics, 50, 29–44. https://doi.org/10.1146/annurev-genet-120215-035429
  • Guan, G., Kobayashi, T., & Nagahama, Y. (2000). Sexually dimorphic expression of two types of DM (Doublesex/Mab-3)-domain genes in a teleost fish, the Tilapia (Oreochromis niloticus). Biochemical and Biophysical Research Communications, 272(3), 662-6. https://doi.org/10.1006/bbrc.2000.2840
  • Inoue, Y., Suenaga, Y., Yoshiura, Y., Moritomo, T., Ototake, M., & Nakanishi, T. (2004). Molecular cloning and sequencing of Japanese pufferfish (Takifugu rubripes) NADPH oxidase cDNAs. Developmental and Comparative Immunology, 28, 911 925. https://doi.org/10.1016/j.dci.2004.03.002
  • Isensee, J., & Noppinger, P.R. (2007). Sexually dimorphic gene expression in mammalian somatic tissue. Gender Medicine, 4(2), 75-95. https://doi.org/10.1016/S1550-8579(07)80049-0
  • Kim, J.H., Rhee, J.S., Lee, J.S., Dahms, H.U., Lee, J., Han, K.N., & Lee, J.S. (2010). Effect of cadmium exposure on expression of antioxidant gene transcripts in the river pufferfish, Takifugu obscurus (Tetraodontiformes). Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 152(4), 473 9. https://doi.org/10.1016/j.cbpc.2010.08.002
  • Kim, C.H., Kim, E.J., & Nam, Y.K. (2021). Superoxide dismutase multigene family from a primitive chondrostean sturgeon, Acipenser baerii: Molecular characterization, evolution, and antioxidant defense during development and pathogen infection. Antioxidants (Basel), 10(2), 232. https://doi.org/10.3390/antiox10020232
  • Koh, C.G., Oon, S.H., & Brenner, S. (1997). Serine/threonine phosphatases of the pufferfish, Fugu rubripes. Gene, 198(1–2), 223-228. https://doi.org/10.1016/S0378-1119(97)00318-1
  • Koop, B.F., & Nadeau, J.H. (1996). Pufferfish and new paradigm for comparative genome analysis. Proceedings of the National Academy of Sciences of the United States of America, 93(4), 1363-5. https://doi.org/10.1073/pnas.93.4.1363
  • Lee, J.H., Kondo, H., Sato, S., Akimoto, S., Saito, T., Kodama, M., & Watabe, S. (2007). Identification of novel genes related to tetrodotoxin intoxication in pufferfish. Toxicon, 49(7), 939 53. https://doi.org/10.1016/j.toxicon.2007.01.008
  • Matzuk, M.M., Dionne, L., Guo, Q., Kumar, R.T., & Russell, M. (1998). Ovarian function in superoxide dismutase 1 and 2 knockout mice. Endocrinology, 139(9), 4008 4011. https://doi.org/10.1210/endo.139.9.6289
  • Remsen, D. (2016). The use and limits of scientific names in biological informatics. ZooKeys, 207 223. https://doi.org/10.3897/zookeys.550.9546
  • Roest Crollius, H., Jaillon, O., Dasilva, C., Ozouf-Costaz, C., Fizames, C., Fischer, C., Bouneau, L., Billault, A., Quétier, F., Saurin, W., Bernot, A., & Weissenbach, J. (2000). Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Research, 10 7, 939-49. https://doi.org/10.1101/GR.10.7.939
  • Rothenburg, S., Deigendesch, N., Dey, M., Dever T.E. & Tazi, L. (2008). Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: Varying the number of double-stranded RNA binding domains and lineage-specific duplications, BMC Biology, 6, 12 https://doi.org/10.1186/1741-7007-6-12
  • Sheng, Y., Abreu, I.A., Cabelli, D.E., Maroney, M.J., Miller, A.F., Teixeira, M., & Valentine, J.S. (2014). Superoxide dismutases and superoxide reductases. Chemical Reviews, 114, 3854-3918. https://doi.org/10.1021/cr4005296
  • Sheraz, A., Zhu, H., Dong, Q., Wang, T., Zong, S., Wang, H., Ge, L., & Wu, T. (2023). The superoxide dismutase (SOD) genes family mediates the response of Nilaparvata lugens to jinggangmycin and sugar. Frontiers in Physiology, 10(14), 1197395. https://doi.org/10.3389/fphys.2023.1197395
  • Stump, E., Ralph, G.M., Comeros-Raynal, M.T., Matsuura, K., & Carpenter, K.E. (2018). Global conservation status of marine pufferfishes (Tetraodontiformes: Tetraodontidae). Global Ecology and Conservation, 14, e00388. https://doi.org/10.1016/j.gecco.2018.e00388
  • Taşbozan, O., Erbaş, C., Bayır, M., Özdemir, E., & Bayır, A. (2022). Identification, characterization and nutritional regulation of fatty acid-binding protein (fabp) genes by vegetable oils in European seabass (Dicentrarchus labrax) reared in low water temperatures. Aquaculture Research, 53(18), 6683-6699. https://doi.org/10.1111/are.16137
  • Thompson, J.D., Higgins, D.G., & Gibson, T.J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  • Uzun, B.N., & Bayır, M. (2023). Bioinformatics studies and examining the tissue distribution of glutathione reductase and glucose-6-phosphate dehydrogenase genes to investigate gender differences in differences in stress tolerance in zebrafish (Danio rerio). Marine Science and Technology Bulletin, 12(3), 352 369. https://doi.org/10.33714/masteb.1337231
  • Wang, W., Xia, M.X., Chen, J., Yuan, R., Deng, F.N., & Shen, F.F. (2016). Gene expression characteristics and regulation mechanisms of superoxide dismutase and its physiological roles in plants under stress. Biochemistry (Moscow), 81(5), 465 80. https://doi.org/10.1134/S0006297916050047
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There are 36 citations in total.

Details

Primary Language English
Subjects Fish Physiology and Genetics
Journal Section Articles
Authors

Büşra Kaya 0000-0003-2913-4136

Mehtap Bayır 0000-0002-7794-1058

Project Number FYL-2021-9735
Early Pub Date December 9, 2024
Publication Date December 11, 2024
Submission Date June 3, 2024
Acceptance Date September 23, 2024
Published in Issue Year 2024 Volume: 41 Issue: 4

Cite

APA Kaya, B., & Bayır, M. (2024). Computational analysis of superoxide dismutase genes (sod1, sod2, and sod3) and comprehensive tissue-specific gene expression profiling in Tetraodon (Tetraodon nigroviridis). Ege Journal of Fisheries and Aquatic Sciences, 41(4), 261-272. https://doi.org/10.12714/egejfas.41.4.02