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

Büşra Kaya; Mehtap Bayır

doi:10.12714/egejfas.41.4.02

TR EN

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

Öz

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).

Anahtar Kelimeler

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

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

Supporting Institution

Atatürk Üniversitesi

Project Number

FYL-2021-9735

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.

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Details

Primary Language

English

Subjects

Fish Physiology and Genetics

Journal Section

Research Article

Authors

Büşra Kaya
0000-0003-2913-4136
Türkiye

Mehtap Bayır ^*
0000-0002-7794-1058
Türkiye

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 Number: 4

DOI

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

IZ

https://izlik.org/JA58YL47XD

Cite

RIS / Bibtex

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