Portal de Periódicos da CAPES

Combining RNA-seq and ddRAD-seq to SNP discovery of a highly migratory and apex predator

2019; Frontiers Media; Volume: 6; Linguagem: Inglês

10.3389/conf.fmars.2019.08.00119

2296-7745

Rodrigo R. Domingues, Vito A. Mastrochirico-Filho, Natália J. Mendes, Diogo Teruo Hashimoto, Rui Coelho, Vanessa Cruz, Agostinho Antunes, Fausto Foresti, Fernando Fernandes Mendonça,

Fish Biology and Ecology Studies

Event Abstract Back to Event Combining RNA-seq and ddRAD-seq to SNP discovery of a highly migratory and apex predator Rodrigo R. Domingues1, 2, 3*, Vito A. Mastrochirico-Filho4, NATALIA J. MENDES4, Diogo Hashimoto4, Rui Coelho5, Vanessa P. Cruz6, Agostinho Antunes2, 7, Fausto Foresti6 and Fernando F. Mendonca8 1 Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Portugal 2 Faculdade de Ciências, Universidade do Porto, Portugal 3 Universidade Federal de São Paulo (UNIFESP), Brazil 4 Centro de Aquicultura, Universidade Estadual Paulista, Brazil 5 Instituto Português do Mar e da Atmosfera, Portugal 6 Instituto de Biociências, Universidade Estadual Paulista, Brazil 7 Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Portugal 8 Universidade Federal de São Paulo (UNIFESP), Brazil 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 and ecology at molecular level is still incipient. Therefore, we combined two massive parallel sequencing approaches, RNA sequencing (RNA-seq) and double digest restriction site-associated DNA sequencing (ddRAD-seq), for single nucleotide polymorphisms (SNPs) discovery in the shortfin mako. A total of four individuals of the shortfin mako (four liver tissue and three eye tissue) were used to RNA-seq library preparation, whereas 34 individuals from five location of the Atlantic Ocean were used to ddRAD-seq library preparation. Both libraries were sequenced by Illumina paired-end sequencing technology (Hiseq 4000). A total of 89,95 Gb raw reads were obtained from RNA-seq. 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. In total, 119,121,972 raw paired-end reads were generated from ddRad-seq sequencing approach. After demultiplex and triming process, ten individuals had low read numbers and were removed from further bioinformatics analyses. Twenty-four samples obtained high quality to further analysis and yielded a total of 88,699,853 paired-end reads. For RNA-seq a total of 129,663 putative single nucleotide polymorphisms (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 annotated SNPs were selected. For ddRAD-seq, after filtering process, taking into account missing data rate, minor allele frequency, quality and deep sequencing, a total of 405 SNPs remained. Our results provide valuable sequence resources for future functional and populational studies of the globally vulnerable shortfin mako shark. Acknowledgements FAPESP (#14/19740-7 ;#17/2420-8; #18/21319-9) Keywords: Isurus oxyrinchus, next generation sequencing, Single nucleotide polymorphism, conservation, Sharks Conference: XX Iberian Symposium on Marine Biology Studies (SIEBM XX) , Braga, Portugal, 9 Sep - 12 Sep, 2019. Presentation Type: Poster Presentation Topic: Fisheries, Aquaculture and Biotechnology Citation: Domingues RR, Mastrochirico-Filho VA, MENDES NJ, Hashimoto D, Coelho R, Cruz VP, Antunes A, Foresti F and Mendonca FF (2019). Combining RNA-seq and ddRAD-seq to SNP discovery of a highly migratory and apex predator. Front. Mar. Sci. Conference Abstract: XX Iberian Symposium on Marine Biology Studies (SIEBM XX) . doi: 10.3389/conf.fmars.2019.08.00119 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: 15 Jun 2019; Published Online: 27 Sep 2019. * Correspondence: Dr. Rodrigo R Domingues, Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal, 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 A Mastrochirico-Filho NATALIA J MENDES Diogo Hashimoto Rui Coelho Vanessa P Cruz Agostinho Antunes Fausto Foresti Fernando F Mendonca Google Rodrigo R Domingues Vito A 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 A Mastrochirico-Filho NATALIA J MENDES Diogo Hashimoto Rui Coelho Vanessa P Cruz Agostinho Antunes Fausto Foresti Fernando F Mendonca PubMed Rodrigo R Domingues Vito A 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.