Bioinformatics in marine ecotoxicology: transcriptome of the amphipod Tiburonella viscana

• Grant number: 24/00963-8
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Start date: May 01, 2024
• End date: August 31, 2024
• Field of knowledge: Physical Sciences and Mathematics - Oceanography - Biological Oceanography
• Principal Investigator: Lucas Buruaem Moreira
• Grantee: Olívio de Araujo Netto
• Supervisor: Tomaso Patarnello
• Host Institution: Instituto do Mar (IMar). Universidade Federal de São Paulo (UNIFESP). Campus Baixada Santista. Santos , SP, Brazil
• Institution abroad: Università Degli Studi Di Padova, Campus Agrípolis - Legnaro, Italy
• Associated to the scholarship: 22/14868-1 - Whole transcriptome analysis of the burrowing amphipod Tiburonella viscana exposed to contaminated sediments., BP.MS

Abstract

Marine pollution is a major threat to biodiversity, and toxicity tests are important to describe and identify environmental risks. Next-generation sequencing (NGS) techniques such as transcriptomics allow the decoding of molecular mechanisms of toxicity and specific biomarkers, supporting the description of initiating events of adverse outcome pathways (AOP), essential for monitoring, pollution control, and remediation. To this end, training human resources is essential for consolidating bioinformatics in marine ecotoxicology. Therefore, the present project aims to train the student for the development of bioinformatics analyses of the transcriptomes of the burrowing amphipod T. viscana, one of the main models used in Brazil.Toxicity tests were carried out in the laboratory, and the RNA from the organisms was extracted and sequenced on the Illumina NextSeq platform, generating 34 transcriptomes. Then, the following analysis steps will be carried out during training: fragment quality, elimination of ribosomal RNAs, de novo assembly, categorization of expressed genes, functional annotation, and plotting differentially expressed genes. At the end of the training, the knowledge acquired will be included in a postgraduate course.