De novo transcriptome assembly, annotation and SNP discovery of the shortfin mako (Isurus oxyrinchus)

Abstract

Event Abstract Back to Event De novo transcriptome assembly, annotation and SNP discovery of the shortfin mako (Isurus oxyrinchus) Rodrigo R. Domingues1, 2*, Vito Antônio Mastrochirico-Filho3, Natalia J. Mendes3, Diogo Hashimoto3, Rui Coelho4, Vanessa P. Cruz5, Agostinho Antunes6, 7, Fausto Foresti5 and Fernando F. Mendonca2 1 Federal University of São Paulo, Brazil 2 Federal University of São Paulo, Brazil 3 Centro de Aquicultura, Universidade Estadual Paulista, Brazil 4 Portuguese Institute of Ocean and Atmosphere (IPMA), Portugal 5 Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista – UNESP, Brazil 6 Interdisciplinary Center for Marine and Environmental Research, Abel Salazar Institute of Biomedical Sciences, University of Porto, Portugal 7 Departament of Biology, Faculty of Sciences, University of Porto, Portugal The shortfin mako, Isurus oxyrinchus is an oceanic pelagic shark species found worldwide in tropical and subtropical waters. It is one of the most frequently shark caught by pelagic longline fisheries, and despite its commercial importance and ecological significance, the understanding of its biology at molecular level is still incipient. Therefore, we used a deep RNA sequencing analysis of the eye and liver tissue from four shortfin mako individuals to characterize the genes of both organs. A total of 89,95 Gb raw reads were obtained by Illumina paired-end sequencing technology (Hiseq 4000). De novo transcriptome from eye and liver yielded a total of 506,686,525 reads and 336,210 contigs. A total of 274,218 and 310, 628 contigs were mapped for eye and liver, respectively, and 37,227 (11.04%) sequences were successfully annotated based on sequence similarities against the Uni-Prot, the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the NCBI non-redundat (NR) protein database. Of these, 31,479 (84.55%) sequences exhibited gene ontology term, which 86.068 (47.8%) were associated with biological process, 55,194 (30.6%) with molecular function, and 39,175 (21.6%) with cellular component. The most frequent terms were: cellular process, single-organism process, and metabolic process for biological process, binding, catalytic activity, and transporter activity for molecular function, and cell, organelle, and membrane for cellular component. In addition, 1,801 genes were found associated to the imune system, 1,090 to growth, 520 to behaviour, and 344 to reproduction. A total of 129,663 putative single nucleotide polymorphism (SNPs) were found in shortfin mako shark. Among them, 78, 598 were putative annotated SNPs, with 14,842 (19%) in coding regions and 63,756 (81%) in non-coding regions. After filtering procedure 1,166 SNPs were selected. Our results provide valuable sequence resources for future functional and populational studies of the globally vulnerable shortfin mako shark. Figure 1 Acknowledgements Fundação de Amparo a Pesquisa do Estado de São Paulo - FAPESP (14/19740-7, 2018/21319-9, 2017/02420-8) Keywords: shark, RNAseq, gene annotation, snps, conservation Conference: XVI European Congress of Ichthyology, Lausanne, Switzerland, 2 Sep - 6 Sep, 2019. Presentation Type: Oral Topic: GENETICS, GENOMICS AND PHYSIOLOGY Citation: Domingues RR, Mastrochirico-Filho V, Mendes NJ, Hashimoto D, Coelho R, Cruz VP, Antunes A, Foresti F and Mendonca FF (2019). De novo transcriptome assembly, annotation and SNP discovery of the shortfin mako (Isurus oxyrinchus). Front. Mar. Sci. Conference Abstract: XVI European Congress of Ichthyology. doi: 10.3389/conf.fmars.2019.07.00050 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 24 May 2019; Published Online: 14 Aug 2019. * Correspondence: Dr. Rodrigo R Domingues, Federal University of São Paulo, São Paulo, Brazil, domingues.pesca@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Rodrigo R Domingues Vito Antônio Mastrochirico-Filho Natalia J Mendes Diogo Hashimoto Rui Coelho Vanessa P Cruz Agostinho Antunes Fausto Foresti Fernando F Mendonca Google Rodrigo R Domingues Vito Antônio Mastrochirico-Filho Natalia J Mendes Diogo Hashimoto Rui Coelho Vanessa P Cruz Agostinho Antunes Fausto Foresti Fernando F Mendonca Google Scholar Rodrigo R Domingues Vito Antônio Mastrochirico-Filho Natalia J Mendes Diogo Hashimoto Rui Coelho Vanessa P Cruz Agostinho Antunes Fausto Foresti Fernando F Mendonca PubMed Rodrigo R Domingues Vito Antônio Mastrochirico-Filho Natalia J Mendes Diogo Hashimoto Rui Coelho Vanessa P Cruz Agostinho Antunes Fausto Foresti Fernando F Mendonca Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.