SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms

  • Phillip A. MorinEmail author
  • Andrew D. Foote
  • Christopher M. Hill
  • Benoit Simon-Bouhet
  • Aimee R. Lang
  • Marie Louis
Part of the Methods in Molecular Biology book series (MIMB, volume 1712)


Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423–1431, 2004; Morin et al., Trends Ecol Evol 19:208–216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. “Hancock-Hanser et al., Mol Ecol Resour 13:254–268, 2013”) can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.

Key words

Bioinformatics Short read archive Reference-guided assembly Single-nucleotide polymorphism Non-model organisms 



We are grateful to Lisa Komoroske for helpful comments on the manuscript. Blue whale DNA sequencing was generously provided by Tim Harkins and Clarence Lee, Life Technologies, Inc., and by Gerald Pao, Salk Institute for Biological Studies.


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Phillip A. Morin
    • 1
    Email author
  • Andrew D. Foote
    • 2
  • Christopher M. Hill
    • 3
  • Benoit Simon-Bouhet
    • 4
  • Aimee R. Lang
    • 1
  • Marie Louis
    • 5
  1. 1.Southwest Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaUSA
  2. 2.Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUK
  3. 3.Department of Computer ScienceUniversity of MarylandCollege ParkUSA
  4. 4.Centre d’Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La RochelleVilliers-en-BoisFrance
  5. 5.Scottish Oceans InstituteUniversity of St AndrewsSt AndrewsUK

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