Open Access Open Badges Research article

Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata

Eshita Sharma12, Axel Künstner1*, Bonnie A Fraser1, Gideon Zipprich3, Verena A Kottler1, Stefan R Henz1, Detlef Weigel1 and Christine Dreyer1*

Author Affiliations

1 Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany

2 Present address: Bioinformatics and Statistical Genetics Core, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, OX3 7BN Oxford, UK

3 Present address: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany

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BMC Genomics 2014, 15:400  doi:10.1186/1471-2164-15-400

Published: 26 May 2014



Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location of these differentially expressed, or sex-biased, genes is important for understanding inter-sexual divergence under sex-specific selection pressures. Teleost fish provide a unique opportunity to examine this divergence in the presence of variable sex-determination mechanisms of recent origin. The guppy, Poecilia reticulata, displays sexual dimorphism in size, ornaments, and behavior, traits shaped by natural and sexual selection in the wild.


To gain insight into molecular mechanisms underlying the guppy’s sexual dimorphism, we assembled a reference transcriptome combining genome-independent as well as genome-guided assemblies and analyzed sex-biased gene expression between different tissues of adult male and female guppies. We found tissue-associated sex-biased expression of genes related to pigmentation, signal transduction, and spermatogenesis in males; and growth, cell-division, extra-cellular matrix organization, nutrient transport, and folliculogenesis in females. While most sex-biased genes were randomly distributed across linkage groups, we observed accumulation of ovary-biased genes on the sex linkage group, LG12. Both testis-biased and ovary-biased genes showed a significantly higher rate of non-synonymous to synonymous substitutions (dN/dS) compared to unbiased genes. However, in somatic tissues only female-biased genes, including those co-expressed in multiple tissues, showed elevated ratios of non-synonymous substitutions.


Our work identifies a set of annotated gene products that are candidate factors affecting sexual dimorphism in guppies. The differential genomic distribution of gonad-biased genes provides evidence for sex-specific selection pressures acting on the nascent sex chromosomes of the guppy. The elevated rates of evolution of testis-biased and female-biased genes indicate differing evolution under distinct selection pressures on the reproductive versus non-reproductive tissues.

Guppy; de novo transcriptome; Genome-guided transcriptome; Sex-biased genes; Sexual dimorphism; RNA-seq; Coding sequence evolution