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

BMC Genomics

Christine Dreyer¹  Detlef Weigel¹  Stefan R Henz¹  Verena A Kottler¹  Gideon Zipprich²  Bonnie A Fraser¹  Axel Künstner¹  Eshita Sharma³ 

[1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany;Present address: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;Present address: Bioinformatics and Statistical Genetics Core, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, OX3 7BN Oxford, UK

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

Others  :  1217197
DOI  :  10.1186/1471-2164-15-400

 received in 2014-01-06, accepted in 2014-05-09,  发布年份 2014

【 摘 要 】

Background

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.

Results

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 (d_N/d_S) 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.

Conclusions

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.

【 授权许可】

   
2014 Sharma et al.; licensee BioMed Central Ltd.

【 图 表 】

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