Percorrer por autor "Antunes, Agostinho"
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- Building a Portuguese coalition for biodiversity genomicsPublication . Marques, João P.; Alves, Paulo C.; Amorim, Isabel R.; Lopes, Ricardo J.; Moura, Monica; Myers, Eugene; Sim-sim, Manuela; Sousa-Santos, Carla; Alves, M. Judite; Borges, Paulo A. V.; Brown, Thomas; Carneiro, Miguel; Carrapato, Carlos; Ceríaco, Luís M. P.; Ciofi, Claúdio; Silva, Luís P. da; Diedericks, Genevieve; Diroma, Maria Angela; Farelo, Liliana; Formenti, Giulio; Gil, Fátima; Grilo, Miguel; Iannucci, Alessio; Leitão, Henrique G.; Máguas,Cristina; Mc Cartney, Ann M.; Mendes, Sofia L.; Moreno, João M.; Morselli, Marco; Mouton, Alice; Natali, Chiara; Pereira, Fernando; Rego, Rúben M. C.; Resendes, Roberto; Roxo, Guilherme; Svardal, Hannes; Trindade, Helena; Vicente, Sara; Winkler, Sylke; Alvarenga, Marcela; Amaral, Andreia J.; Antunes, Agostinho; Campos, Paula F.; Canario, Adelino; Castilho, Rita; Castro, L. Filipe C.; Crottini, Angelica; Cunha, Mónica V.; Themudo, Gonçalo Espregueira; Esteves, Pedro J.; Faria, Rui; Rodríguez Fernandes, Carlos; Ledoux, Jean-Baptiste; Louro, Bruno; Magalhaes, Sara; Paulo, Octávio S.; Pearson, Gareth Anthony; Pimenta, João; Pina-Martins, Francisco; Santos, Teresa L.; Serrao, Ester A.; Melo-Ferreira, José; Sousa, Vítor C.The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation, or pathogen (re) emergence. The inventory, characterisation, and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures, and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative and its pilot effort to generate reference genomes for European biodiversity has reinforced the establishment of Biogenome Portugal.
- Comparative eye and liver differentially expressed genes reveal monochromatic vision and cancer resistance in the shortfin mako shark (Isurus oxyrinchus)Publication . 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.The shortfin mako, Isurus oxyrinchus is an oceanic pelagic shark found worldwide in tropical and subtropical waters. However, the understanding of its biology at molecular level is still incipient. We sequenced the messenger RNA isolated from eye and liver tissues. De novo transcriptome yielded a total of 705,940 transcripts. A total of 3774 genes were differentially expressed (DEGs), with 1612 in the eye and 2162 in the liver. Most DEGs in the eye were related to structural and signaling functions, including nonocular and ocular opsin genes, whereas nine out of ten most overexpressed genes in the liver were related to tumor suppression, wound healing, and human diseases. Furthermore, DEGs findings provide insights on the monochromatic shark vision and a repertory of cancer-related genes, which may be insightful to elucidate shark resistance to cancer. Therefore, our results provide valuable sequence resources for future functional and population studies.
- 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.