ArticleGenome biology and evolution2020
Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).
Article in Genome biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 48 citations in OpenAlex.
- Article
- Genome-Wide Characterization of Sex-Linked Regions in the Sangzhi Horned Toad (Boulenophrys sangzhiensis) Reveals Complex Sex Determination Mechanisms.Molecular ecology resources · 2026Article
- The next generation of colour pattern genomics.Nature ecology & evolution · 2025Article
- Deep learning reveals the complex genetic architecture of male guppy colouration.Nature ecology & evolution · 2025Article
- New Genome Assemblies for Poeciliidae: A Foundation for Adaptation Studies.Genome biology and evolution · 2025Article
- Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly.Genome research · 2025Article
- Sex Chromosome Evolution: Hallmarks and Question Marks.Molecular biology and evolution · 2024Review
- Improved assembly of the Pungitius pungitius reference genome.G3 (Bethesda, Md.) · 2024Article
- Convergent genomic signatures associated with vertebrate viviparity.BMC biology · 2024Article
- Whole Genome Assembly and Annotation of Blackstripe Livebearer Poeciliopsis prolifica.Genome biology and evolution · 2023Article
- Evolutionary History of the Poecilia picta Sex Chromosomes.Genome biology and evolution · 2023Article
- Master-Key Regulators of Sex Determination in Fish and Other Vertebrates-A Review.International journal of molecular sciences · 2023Review
- Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.Journal of evolutionary biology · 2022Article
- Partial sex linkage and linkage disequilibrium on the guppy sex chromosome.Molecular ecology · 2022Article
- Are plant and animal sex chromosomes really all that different?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Evolution letters · 2022Article
- On the genetic architecture of rapidly adapting and convergent life history traits in guppies.Heredity · 2022Article
- Article
- A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy.Nature communications · 2022Article
- Evolution of the canonical sex chromosomes of the guppy and its relatives.G3 (Bethesda, Md.) · 2022Article
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Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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