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Transcriptomic response of Mytilus galloprovincialis to emerging contaminants: Data analysis workflow
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Introduction: Environmental pollutants such as tetrabromobisphenol A (TBBPA), perfluoroalkyl substances (PFASs) like perfluorooctanoic acid (PFOA), and endocrine-disrupting compounds (EDCs) as 17α-ethinylestradiol (EE2) are commonly detected in coastal ecosystems. The Mediterranean mussel, Mytilus galloprovincialis, is a species of significant ecological and economic importance. Recent genomic studies have revealed an open pan-genome structure, with approximately 25–30% of protein-coding genes varying among individuals due to presence/absence variation (PAV). Assessing their molecular effects on marine organisms requires robust experimental models that reflect realistic exposure scenarios.
Aim: Investigate transcriptomic alterations in M. galloprovincialis following exposure to environmentally relevant concentrations of TBBPA, PFOA, and EE2 under controlled laboratory conditions.
Methods: Adult mussels were collected from Guincho coast (Portugal) and acclimated for 5 days under laboratory conditions (20 ± 1°C; salinity 33 ± 1 g·L⁻¹; pH 8.1). Mussels were then exposed for 28 days to TBBPA (1, 10, 100 µg/L), PFOA (1, 100 µg/L), or EE2 (10, 1000 ng/L), with and unexposed group (control). Each treatment consisted of four biological replicates (two males and two females). At the end of the exposure period, mussels were dissected, and soft tissues were preserved at −80°C. RNA was extracted from whole-body homogenates, and only samples with an RNA Integrity Number (RIN) > 9.0 were selected for sequencing.
Results: RNA libraries were prepared using the Illumina TruSeq Stranded mRNA protocol and sequenced on a NextSeq 2000 platform (2×100 bp paired-end), generating over 85 Gbp of high-quality data (>84% bases with Q30). Raw reads underwent quality control using FastQC and MultiQC. Reads were aligned to the M. galloprovincialis reference genome using the splice-aware aligner STAR. Differential gene expression analysis was performed with DESeq2, and functional interpretation was based on Gene Ontology (GO) and KEGG pathway enrichment.
Conclusion: This approach demonstrates the utility of mussel transcriptomics for ecotoxicogenomic assessment of marine pollution.
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Mytilus galloprovincialis RNA-Seq Emerging Environmental Contaminants Segurança Alimentar