Studi Bioinformatika: Re-Analisis Data RNA-Seq Ekspresi Gen Diferensial Ikan Nila pada Stres Suhu dengan Pendekatan DESeq2

Abstract

Perubahan iklim global menyebabkan peningkatan suhu air yang signifikan dan berdampak langsung terhadap keberlangsungan budidaya ikan nila (Oreochromis niloticus). Penelitian ini bertujuan untuk menganalisis ekspresi gen diferensial ikan nila non-hibrida yang mengalami stres suhu menggunakan pendekatan transkriptomik berbasis RNA-Seq dan metode statistik DESeq2. Dataset RNA-Seq diunduh dari NCBI-SRA, terdiri atas enam sampel hati ikan nila strain GIFT yang dipelihara pada suhu normal (29°C) dan suhu tinggi (37,5°C). Analisis dilakukan melalui serangkaian tahapan bioinformatika, yakni quality control, trimming, alignment ke genom referensi, kuantifikasi ekspresi gen dengan featureCounts, dan analisis diferensial menggunakan DESeq2. Hasil menunjukkan 918 gen yang terekspresi secara signifikan (padj < 0,05; |log2FC| = 1), terdiri atas 502 gen up-regulated dan 416 gen down-regulated. Analisis fungsi gen melalui Gene Ontology dan KEGG mengindikasikan aktivasi jalur biologis yang terkait dengan respons stres, metabolisme energi, dan regulasi sistem imun, termasuk ekspresi gen HSP, sitokin, dan enzim metabolik. Hasil penelitian ini menunjukkan adanya perubahan molekuler sistemik akibat paparan suhu tinggi dan memberikan landasan ilmiah untuk pengembangan strain nila tahan stres suhu melalui pendekatan seleksi berbasis ekspresi gen.

Global climate change has led to increased water temperatures, posing a critical threat to the sustainability of Nile tilapia (Oreochromis niloticus) aquaculture. This study aimed to investigate differential gene expression in non-hybrid Nile tilapia under thermal stress using RNA-Seq and the DESeq2 statistical framework. RNA-Seq datasets were retrieved from NCBI-SRA, consisting of liver samples from GIFT-strain tilapia reared at 29°C (control) and 37.5°C (thermal stress). The bioinformatics workflow included data quality control, trimming, alignment to the reference genome, gene quantification using featureCounts, and differential expression analysis via DESeq2. A total of 918 differentially expressed genes (padj < 0.05; |log2FC| = 1) were identified, comprising 502 up-regulated and 416 down-regulated genes under thermal stress. Functional annotation through Gene Ontology and KEGG pathway analysis revealed the enrichment of stress response pathways, energy metabolism regulation, and immune-related processes, including heat shock proteins, cytokines, and metabolic enzymes. These results demonstrate a systemic molecular response to elevated temperature and provide scientific insight for developing heat-tolerant tilapia strains through gene expression-informed selection strategies.