Browsing by Author "Mendonça, Fernando F."
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- Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)Publication . Domingues, Rodrigo R.; Mastrochirico-Filho, Vito Antonio; Mendes, Natalia J.; Hashimoto, Diogo T.; Coelho, Rui; Antunes, Agostinho; Foresti, Fausto; Mendonça, Fernando F.The shortfin mako, Isurus oxyrinchus, is an oceanic pelagic shark species found worldwide in tropical and subtropical waters. It is frequently caught by pelagic longline fisheries, but despite its commercial importance and ecological significance, little is still known about its biology and ecology at the molecular level. Therefore, we combined two massive parallel sequencing approaches, double digest restriction site-associated DNA sequencing (ddRAD) and RNA sequencing (RNAseq), for single nucleotide polymorphism (SNP) discovery in the shortfin mako. The ddRAD yielded a total of 82,676 putative SNPs. For RNAseq, a total of 129,663 putative SNPs were found. After the stricter filtering procedure, 405 SNPs from ddRAD and 1165 SNPs from RNAseq were retained and suitable for further analysis. Annotation analysis of SNPs from ddRAD revealed a total of 55 gene associated SNP markers, of which 32 SNPs (58.2%) are associated with diseases and defense responses, 9 SNPs (16.4%) are associated with developmental process, and 3 SNPs (5.4%) are present in genes involved in the reproductive function. For RNAseq, 739 SNPs were annotated and associated to relevant functions amongst which 10 SNPs (0.53%) were related with reproduction, 6 SNPs (0.32%) with growth, and 9 (0.48%) with locomotion. Overall, the genotyping of the SNPs was followed by the validation of 255 SNPs from ddRAD and 646 for RNAseq in 31 individuals from the Atlantic and Indian oceans. Our results provide valuable sequence resources for future population genomics analysis, comparative genomics, phylogenomics, and molecular evolution of the globally endangered shortfin mako shark.
- A new map of the tiger shark (Galeocerdo cuvier) genetic population structure in the western Atlantic Ocean: Hypothesis of an equatorial convergence centrePublication . Carmo, Camila B.; Ferrette, Bruno L.S.; Camargo, Sâmia M.; Roxo, Fábio F.; Coelho, Rui; Garla, Ricardo C.; Oliveira, Claudio; Piercy, Andrew N.; Bornatowski, Hugo; Foresti, Fausto; Burgess, George H.; Mendonça, Fernando F.The tiger shark (Galeocerdo cuvier) is a common widespread coastal–pelagic shark species whose population genetic structure has only recently been the object of genetic studies. In this study, the tiger's shark mitochondrial DNA control region was sequenced for a sample of 172 individuals from the western Atlantic and from Australia's east coast in the Pacific Ocean. The results show a moderate variation in genetic diversity (h = 0.615 ± 0.038, π = 0.00184 ± 0.00021) with a strong population structure between Atlantic areas (ΦST = 0.28141, P = 0.00001). The maternal lineage has high site fidelity, which paradoxically is coupled with connectivity across open ocean stretches to Fernando de Noronha Archipelago, which is identified as an important hotspot for this species. These results help with the understanding of what drives the displacement of this shark, at intra‐ and/or inter‐ocean basins levels, and can help inform the implementation of future conservation and management measures. We recommend that the conservation of genetic diversity should be maintained at a global level and its maintenance should be pursued diligently in all populations of tiger shark. As the Fernando de Noronha region in the western Atlantic appears to contain the largest global genetic diversity of the species, this area should be treated as a marine reserve or ecological refuge for the tiger shark.