The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population

PLoS One. 2016 Dec 29;11(12):e0169087. doi: 10.1371/journal.pone.0169087. eCollection 2016.

Abstract

For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (π) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.

MeSH terms

  • Adaptation, Physiological
  • Animals
  • DNA Mutational Analysis
  • Female
  • Genomics*
  • Male
  • Molecular Sequence Annotation
  • Poecilia / genetics*
  • Poecilia / physiology
  • Polymorphism, Single Nucleotide*
  • Sex Chromosomes / genetics
  • Synteny

Grant support

This work was supported by a Gottfried Wilhelm Leibniz Award of the Deutsche Forschungsgemeinschaft and the Max Planck Society. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.