Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata)

Bonnie Fraser*, James R. Whiting, Josephine R. Paris, Cameron J. Weadick, Paul J. Parsons, R Bergero, Deborah Charlesworth, Felix Bemm, Margarete Hoffmann, Verena A. Kottler, Chang Liu, Christine Dreyer, Detlef Weigel

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)


Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male color patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low-predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.

Original languageEnglish
Article numberevaa187
Pages (from-to)1789-1805
Number of pages17
JournalGenome Biology and Evolution
Issue number10
Early online date27 Aug 2020
Publication statusPrint publication - 1 Oct 2020
Externally publishedYes

Bibliographical note

© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


  • Poecilia reticulata
  • genome
  • guppy
  • population genomics
  • sex chromosome


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