Conservation Genetics Resources

, Volume 9, Issue 1, pp 29–33 | Cite as

SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping

  • José Gregorio Martínez
  • Valéria Nogueira Machado
  • Susana J. Caballero-Gaitán
  • Maria da C. Freitas Santos
  • Rodrigo Maciel Alencar
  • Maria Doris Escobar L.
  • Tomas Hrbek
  • Izeni Pires Farias
Technical Note

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 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 

Notes

Acknowledgments

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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12686_2016_610_MOESM1_ESM.pdf (1010 kb)
Supplementary material 1. Online Resource 1 Putative SNPs for the tambaqui Colossoma macropomum 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 1010 KB)
12686_2016_610_MOESM2_ESM.pdf (178 kb)
Supplementary material 2. Online Resource 2 Command lines script file used for running Stacks pipeline programs components (process_radtags.pl, denovo_map.pl and populations.pl) for de novo SNPs genotyping across all individuals (Orinoco and Amazon basins) of the tambaqui Colossoma macropomum. (PDF 178 KB)
12686_2016_610_MOESM3_ESM.txt (556 kb)
Supplementary material 3. Online Resource 3 Variant Call Format (VCF) file from Stacks pipeline (populations.pl) showing the number of samples, allele frequency, genotypes, read depth and genotype likelihood across all individuals (Orinoco and Amazon basins) of the tambaqui Colossoma macropomum. (TXT 555 KB)
12686_2016_610_MOESM4_ESM.txt (43 kb)
Supplementary material 4. Online Resource 4 FST file from the Stacks pipeline (populations.pl) showing the statistic power (Fst), Fisher’s P-value, diversity index (π), AMOVA and others for each one of the 268 recovered SNPs from both Orinoco and Amazon basins tambaqui Colossoma macropomum. (TXT 42 KB)
12686_2016_610_MOESM5_ESM.txt (192 kb)
Supplementary material 5. Online Resource 5 SUMSTATS (summary statistics) file from Stacks pipeline (populations.pl) 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 1530 recovered SNPs from the tambaqui Colossoma macropomum. (TXT 192 KB)

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • José Gregorio Martínez
    • 1
    • 2
    • 3
  • Valéria Nogueira Machado
    • 1
  • Susana J. Caballero-Gaitán
    • 2
  • Maria da C. Freitas Santos
    • 1
    • 3
  • Rodrigo Maciel Alencar
    • 3
  • Maria Doris Escobar L.
    • 4
  • Tomas Hrbek
    • 1
  • Izeni Pires Farias
    • 1
  1. 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/BionorteUniversidade Federal do AmazonasManausBrazil
  2. 2.Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Facultad de Ciencias, Departamento de Ciencias BiológicasUniversidad de los AndesBogotáColombia
  3. 3.Laboratório de Proteômica e Genômica, Programa de Pós-graduação Mestrado em Biotecnologia e Recursos Naturais (MBT), Grupo de Pesquisa em Genética Molecular e CitogenéticaUniversidade do Estado do AmazonasManausBrazil
  4. 4.Programa de Pós-graduação em Recursos PesqueirosUniversidade Federal do AmazonasManausBrazil

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