Use of omics and bioinformatics tools for detect local adaptation of the shortfin mako shark (Isurus oxyrinchus) in the Atlantic and Indian Ocean

• Grant number: 18/21319-9
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: March 04, 2019
• End date: March 03, 2020
• Field of knowledge: Physical Sciences and Mathematics - Oceanography - Biological Oceanography
• Principal Investigator: Fernando Fernandes Mendonça
• Grantee: Rodrigo Rodrigues Domingues
• Supervisor: Agostinho Antunes Pereira
• Host Institution: Instituto de Saúde e Sociedade (ISS). Universidade Federal de São Paulo (UNIFESP). Campus Baixada Santista. Santos , SP, Brazil
• Institution abroad: Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Portugal
• Associated to the scholarship: 17/02420-8 - High-tech conservation: combining oceanography, transcriptome and genomics to assess population genetic connectivity and local adaptation of the highly migratory Mako shark (Isurus oxyrinchus) in the Atlantic Ocean, BP.PD

Abstract

In the initial post-doctoral project proposal submitted to FAPESP, was aimed to characterize the transcriptome and to perform a population genomic study of one of the largest predators in the marine environment, with a broad geographical distribution, and ecological and commercial interest, the mako shark (Isurus oxyrinchus). In addition, the initial proposal aimed at training human resources in the field of bioinformatics and genomics. The laboratorial step, using new generation sequencing techniques - NGS (RNA-seq and ddRADseq), yielded massive amounts of sequencing with more than 42 784 019 million sequences of RNA-seq for the characterization of the transcriptome, and 119 121 972 million sequences of ddRADseq for population genomic study. Thus, the second stage of this project involves the treatment of these data through bioinformatics techniques for subsequent analyzes that may to shed light on biological and ecological significance to the mako shark. Therefore, this project aims: (i) training in bioinformatics to treat sequencing of RNA-seq and ddRADseq, (ii) to identify genes and their associations with biological, physiological and molecular functions, (iii) to select genes that allow inferences on local adaptation as well as an extensive population genomic study in two large oceanic basins, Atlantic and Indian Oceans. At the end of this period abroad, it is expected to obtain new results for this species, which will result in publications in high impact scientific journals, as well as a solid formation of the candidate in genomics and bioinformatics, and collaborations with renowned researchers from abroad who have worked in the frontier of knowledge in this area of research.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DOMINGUES, RODRIGO RODRIGUES; BUNHOLI, INGRID VASCONCELLOS; PINHAL, DANILLO; ANTUNES, AGOSTINHO; MENDONCA, FERNANDO FERNANDES. From molecule to conservation: DNA-based methods to overcome frontiers in the shark and ray fin trade. CONSERVATION GENETICS RESOURCES, v. 13, n. 2, p. 231-247, JUN 2021. (18/21319-9, 17/02420-8)

DOMINGUES, RODRIGO R.; MASTROCHIRICO-FILHO, VITO ANTONIO; MENDES, NATALIA J.; HASHIMOTO, DIOGO T.; COELHO, RUI; DA CRUZ, VANESSA PAES; ANTUNES, AGOSTINHO; FORESTI, FAUSTO; MENDONCA, FERNANDO F.. Comparative eye and liver differentially expressed genes reveal monochromatic vision and cancer resistance in the shortfin mako shark (Isurus oxyrinchus). Genomics, v. 112, n. 6, p. 4817-4826, NOV 2020. (17/02420-8, 14/19740-7, 18/21319-9)