SNPs markers for the heavily overfished tambaqui Colossoma macropomum , a Neotropical fish, using next-generation sequen
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TECHNICAL NOtE
SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping José Gregorio Martínez1,2,3 · Valéria Nogueira Machado1 · Susana J. Caballero-Gaitán2 · Maria da C. Freitas Santos1,3 · Rodrigo Maciel Alencar3 · Maria Doris Escobar L.4 · Tomas Hrbek1 · Izeni Pires Farias1
Received: 23 August 2016 / Accepted: 30 August 2016 © Springer Science+Business Media Dordrecht 2016
Abstract 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
Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0610-3) contains supplementary material, which is available to authorized users.
José Gregorio Martínez [email protected] 1
Laboratório de Evolução e Genética Animal, Instituto de Ciências Biológicas, Departamento de Genética, Programa de Pós-graduação em Biodiversidade e Biotecnologia da Amazônia Legal/Bionorte, Universidade Federal do Amazonas, Av. Rodrigo Octávio Jordão Ramos, 3000, 69077-000 Manaus, Amazonas, Brazil
2
Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Cra 1 Nº 18A- 12, Código Postal 4-72, Bogotá, Colombia
3
Laboratório de Proteômica e Genômica, Programa de Pósgraduação Mestrado em Biotecnologia e Recursos Naturais (MBT), Grupo de Pesquisa em Genética Molecular e Citogenética, Universidade do Estado do Amazonas, Manaus, Amazonas 69065-001, Brazil
4
Programa de Pós-graduação em Recursos Pesqueiros, Universidade Federal do Amazonas, Manaus, Amazonas 69065-001, Brazil
could be useful for conservation/population genetics using traditional PCR-based genotyping methods. Keywords De novo SNPs development · Conservation/population genomics · IonTorrent PGM · Orinoco/Amazon basins
The tambaqui/cachama negra, Colossoma macropomum, is the largest characin in South-America and the second largest Neotropical fish, reaching at least one meter in total length and 30 kg in weight (Goulding and Carvalho 1982). This species is widely distributed throughout the western and central Amazon and Orinoco Basins (Isaac and Ruffino 1996; Araujo-Lima and Goulding 1997). The tambaqui is commercially overexploited, being one of the ten most captured species in the Amazon (Ruffino and Isaac 1994). In the last third of the twentieth century, the average length of adult individuals decreased from 60 to 45 cm, and its contribution me
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