SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping
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We developed nuclear SNPs for the heavily overfished tambaqui/cachama negra Colossoma macropomum using next-generation sequencing-based genotyping. We created a reduced-representation library for 30 individuals from Orinoco and Amazon basins following the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the software Stacks. We detected 22,476 tags characterized by 7,181 polymorphic sites, recovering 177 loci (268 SNPs) shared between both basins. A significant difference in the allelic frequencies was observed between basins for a subset of these SNPs. Thirty-nine SNPs could be useful for conservation/population genetics using traditional PCR-based genotyping methods.
KeywordsDe novo SNPs development Conservation/population genomics IonTorrent PGM Orinoco/Amazon basins
This work was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and PRONEX/FAPEAM from Brazil, and the Departamento Administrativo de Ciencia, Tecnolgía e Innovación (COLCIENCIAS) from Colombia (Grant Number 490682/2010-3). In Brazil, permission to collect tissue samples was granted by SISBIO/IBAMA, and in Colombia by ANLA (to Universidad de los Andes). We are grateful with the Laboratório de Tecnologias de DNA, specially with Spartaco Astolfi Filho and Enedina Nogueira by the technical support during sequencing process. IPF and TH were supported by a Bolsa de Pesquisa scholarship from CNPq during this study. JGM was supported by postdoctoral scholarship from CAPES in the MBT program of UEA.
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Conflict of interest
The authors declare that they have no conflict of interest.
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