Conservation Genetics Resources

, Volume 8, Issue 4, pp 415–418 | Cite as

De novo SNP markers development for the Neotropical gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing-based genotyping

  • José Gregorio Martínez
  • Susana Josefina Caballero-Gaitán
  • Diana Sánchez-Bernal
  • Enedina Nogueira de Assunção
  • Spartaco Astolfi-Filho
  • Tomas Hrbek
  • Izeni Pires Farias
Technical Note


We generated for the first time nuclear SNP loci for the commercially exploited gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing. We implemented double-digest-Restriction-Associated-DNA-based de novo SNP genotyping for 30 individuals (Orinoco and Amazon basins) using the IonTorrent PGM. It was analyzed the sequence reads using the Stacks pipeline. We detected 18,772 tags with 6170 polymorphic sites and 91 SNPs recovered for both basins. A significant divergence in the allele frequencies was observed between basins for some of those SNPs. Information about diversity and other statistics index are presented for these SNPs. Some of them (23) could be useful for population and conservation genetics of this species using traditional PCR-based genotyping methods.


SNPs Gilded catfish IonTorrent PGM Population/conservation genomics 



This study was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) of Brazil, and the Departamento Administrativo de Ciencia, Tecnolgía e Innovación (COLCIENCIAS) of Colombia (code: 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). This study is part of JGM’s doctoral thesis in the Biotechnology program of UFAM. JGM was supported by a Beca de Formación doctoral scholarship Francisco José de Caldas from COLCIENCIAS, and IPF and TH were supported by a Bolsa de Pesquisa scholarship from CNPq during this study.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12686_2016_584_MOESM1_ESM.pdf (717 kb)
Online Resource 1 Putative SNPs for the gilded catfish Brachyplatystoma rousseauxii samples from the Orinoco and Amazon basins obtained with Stacks pipeline. Includes SNP consensus tag IDs, SNP position in the tag, the most likely SNP, and the source population with their geographical coordinates (PDF 716 kb)
12686_2016_584_MOESM2_ESM.pdf (186 kb)
Online Resource 2 Command lines script file used for running Stacks pipeline programs components (, and for de novo SNPs genotyping across all individuals (Orinoco and Amazon basins) of the gilded catfish Brachyplatystoma rousseauxii. (PDF 185 kb)
12686_2016_584_MOESM3_ESM.txt (337 kb)
Online Resource 3 Variant Call Format (VCF) file from Stacks pipeline ( showing the number of samples, allele frequency, genotypes, read depth and genotype likelihood across all individuals (Orinoco and Amazon basins) of the gilded catfish Brachyplatystoma rousseauxii. (TXT 336 kb)
12686_2016_584_MOESM4_ESM.txt (16 kb)
Online Resource 4 FST file from Stacks pipeline ( showing the statistic power (Fst), Fisher’s P-value, diversity index (π), AMOVA and others for each one of the 91 recovered SNPs from both Orinoco and Amazon basins gilded catfish Brachyplatystoma rousseauxii. (TXT 15 kb)
12686_2016_584_MOESM5_ESM.txt (90 kb)
Online Resource 5 SUMSTATS (summary statistics) file from Stacks pipeline ( showing the loci, SNP position in the tag loci, population source, most frequent allele, alternative allele, frequency of the most frequent allele, number of individuals from which the SNP was recovered, heterozygosis and others for each one of the initial 849 recovered SNPs from the gilded catfish Brachyplatystoma rousseauxii. (TXT 89 kb)


  1. Araujo-Lima CARM, Ruffino ML (2003) Migratory fishes of South America: biology, fisheries and conservation status. IDRC/World Bank, WashingtonGoogle Scholar
  2. Barthem RB, Fabré NN (2004) Biologia e diversidade dos recursos pesqueiros da amazônia. In: Ruffinno ML (ed) A pesca e os recursos pesqueiros na Amazonia. Projeto manejo dos recursos naturais de Várzea. IBAMA MMA/PROVÁRZEA, pp 11–55Google Scholar
  3. Barthem R, Goulding M (1997) The catfish connection: ecology, migration, and conservation of Amazon predators. Columbia University Press, New YorkGoogle Scholar
  4. Batista J, Alves-Gomes J (2006) Phylogeography of Brachyplatystoma rousseauxii (Siluriformes–Pimelodidae) in the Amazon Basin offers preliminary evidence for the first case of “homing” for an Amazonian migratory catfish. Genet Mol Res 5:723–740PubMedGoogle Scholar
  5. Batista JS, Farias IP, Formiga-Aquino K et al (2009) DNA microsatellite markers for “dourada” (Brachyplatystoma rousseauxii, Siluriformes: Pimelodidae), a migratory catfish of utmost importance for fisheries in the Amazon: development, characterization and inter-specific amplification. Conserv Genet Resour 2:5–10CrossRefGoogle Scholar
  6. Carvajal-Vallejos FM, Duponchelle F, Desmarais E et al (2014) Genetic structure in the Amazonian catfish Brachyplatystoma rousseauxii: influence of life history strategies. Genetica 142:323–336CrossRefPubMedGoogle Scholar
  7. Catchen JM, Amores A, Hohenlohe P et al (2011) Stacks: building and genotyping Loci de novo from short-read sequences. G3 Bethesda 1:171–182CrossRefPubMedPubMedCentralGoogle Scholar
  8. Davey J, Blaxter M (2010) RADseq: next-generation population genetics. Brief Funct Genom 9:416–423CrossRefGoogle Scholar
  9. Goulding M (1980) The Fishes and the forest: explorations in Amazonian natural history. California University Press, BerkelyGoogle Scholar
  10. Kearse M, Moir R, Wilson A et al (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649CrossRefPubMedPubMedCentralGoogle Scholar
  11. Peterson BK, Weber JN, Kay EH et al (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7(5):e37135CrossRefPubMedPubMedCentralGoogle Scholar
  12. Reis R, Lima F (2009) Brachyplatystoma rousseauxii. The IUCN red list of threatened species 2009. e.T167648A6362510. doi: 10.2305/IUCN.UK.2009-2.RLTS.T167648A6362510.en
  13. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Springs Harbor Laboratory Press, New YorkGoogle Scholar
  14. Seeb JE, Carvalho G, Hauser L et al (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 1:1–8CrossRefGoogle Scholar
  15. Tautz D, Ellegren H, Weigel D (2010) Next generation molecular ecology. Mol Ecol 19:1–3CrossRefPubMedGoogle Scholar
  16. Toonen RJ, Puritz JB, Forsman ZH et al (2013) ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 1:e203CrossRefPubMedPubMedCentralGoogle Scholar
  17. You FM, Huo N, Gu YQ et al (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinform 9:253CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • José Gregorio Martínez
    • 1
    • 2
    • 3
  • Susana Josefina Caballero-Gaitán
    • 3
  • Diana Sánchez-Bernal
    • 3
  • Enedina Nogueira de Assunção
    • 4
  • Spartaco Astolfi-Filho
    • 4
  • Tomas Hrbek
    • 1
  • Izeni Pires Farias
    • 1
  1. 1.Laboratório de Evolução e Genética Animal, Departamento de GenéticaUniversidade Federal do AmazonasManausBrazil
  2. 2.Laboratório de Proteômica e Genômica, Programa de Pós-graduação Mestrado em Biotecnologia e Recursos Naturais (MBT), Grupo de Pesquisa em Genética Molecular e CiotegenéticaUniversidade do Estado do AmazonasManausBrazil
  3. 3.Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Facultad de Ciencias, Departamento de Ciencias BiológicasUniversidad de los AndesBogotáColombia
  4. 4.Laboratório de Tecnologias de DNA, Centro de Apoio MultidisciplinarUniversidade Federal do AmazonasManausBrazil

Personalised recommendations