Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 May 26;15(1):400.
doi: 10.1186/1471-2164-15-400.

Transcriptome Assemblies for Studying Sex-Biased Gene Expression in the Guppy, Poecilia Reticulata

Affiliations
Free PMC article

Transcriptome Assemblies for Studying Sex-Biased Gene Expression in the Guppy, Poecilia Reticulata

Eshita Sharma et al. BMC Genomics. .
Free PMC article

Abstract

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 (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.

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.

Figures

Figure 1
Figure 1
Assembly of the guppy reference transcriptome. (A) Flowchart describing read summary, assembly strategy, and assembler comparison. The high quality paired reads from each sequenced dataset, non-barcoded (orange) and barcoded (green), were assembled using genome-independent (Trinity, GIA, red) and genome-guided (Cufflinks, GGA, blue) assemblers. Venn diagram shows the total number of protein sequence orthologs identified between at least two species using translated sequences from the two guppy assemblies (red, blue), and protein sequence databases from eight teleosts, mouse, and human (yellow); (B) Inset (dotted yellow, bottom left) shows an alternate view of the ortholog comparisons. Barplots show the number of orthologs identified in two-way reciprocal best blast-hit comparison between platyfish, tilapia, medaka, stickleback, takifugu, tetraodon, zebrafish, cod, human, and mouse proteins. The stacked bars show the number of orthologs common between GGA and GIA (purple), unique to GGA (blue) and unique to GIA (red); (C) Inset rectangle (dotted blue, bottom right) summarizes the steps for merging predicted CDS from both assemblies and functional annotation of the guppy reference transcriptome (GRT).
Figure 2
Figure 2
Phenotypic sexual dimorphism in the guppy. Males (top) are smaller than females (bottom) and have complex color patterns on the body. The encircled region (white outline) indicates the tissues that were used for preparing the barcoded libraries, 1) brain and eyes; 2) Male testis and female ovary; and 3) tail.
Figure 3
Figure 3
Quantitative differences in gene expression between sexes. Male to female expression ratios (log2FC, Fold-change: Male/Female) plotted against the average expression intensity (log2CPM, Counts per million) in (A) brain, (C) tail, and (E) gonads. Genes with greater than median-fold bias (FDR < 0.1) are shown in red while the others are shown by black dots or smoothened. The blue lines mark a 4-fold difference in expression between the sexes. Genes with sex-limited expression are underlined in black (E). The number of male-biased and female-biased genes in each comparison is mentioned at the top-right and bottom-right respectively in each figure. Heatmaps showing the mean centered log2FPKM (Fragments per kilo base per million) for the highest differentially expressed genes (FDR < 0.001) and a 1.5 fold-change in the brain (B), 1.7 fold-change in the tail (D), and 32 fold-change in the gonad (F). The top 30 genes that show sex-biased expression in each tissue are listed and ranked by fold-change in grey text boxes at the left (female-biased genes) and at the right (male-biased genes).
Figure 4
Figure 4
Male-biased expression of guppy pigmentation orthologs in tail. Barplots show male to female expression ratios (log2 FC: Male/Female) in tail tissue for differentially expressed candidate pigmentation genes (FDR < 0.1). Horizontal grey dotted line marks a 4-fold change in gene expression. Candidate gene names and linkage groups are specified at the bottom.
Figure 5
Figure 5
Linkage group distributions of sex-biased genes. Distribution of percentage of testis-biased (blue) and ovary-biased (pink) genes over all gonad-expressed genes per linkage group (LG). Sex-biased genes were identified as those that show significant difference in expression (FDR < 0.05) above the 1.2 fold-change (log2FC: Male/Female). LGs with a significant over- or under-representation of sex-biased genes are marked with an asterisk (p < 0.05, after multiple correction).
Figure 6
Figure 6
Nucleotide substitution rates in sex-bias genes per tissue. Mean values with 95% confidence intervals for rate of nucleotide substitutions in coding sequences. (A) d N /d S ratios; (B) d N; and (C) d S. Male-biased (MB: blue), female-biased (FB: pink), and unbiased (UB: yellow) genes for brain, gonad, and tail. Asterisks above the boxplots indicate a significant difference in substitution rate was found between the sex-biased and unbiased genes using Mann–Whitney U test for non-parametric distributions (**** p < 0.0001; *** p < 0.001; ** p <0.01; * p < 0.05).

Similar articles

See all similar articles

Cited by 23 articles

See all "Cited by" articles

References

    1. Rowe L, Day T. Detecting sexual conflict and sexually antagonistic coevolution. Philos Trans R Soc Lond Ser B Biol Sci. 2006;361(1466):277–285. doi: 10.1098/rstb.2005.1788. - DOI - PMC - PubMed
    1. Lande R. Sexual dimorphism, sexual selection, and adaptation in polygenic characters. Evolution; Int J of organic evolution. 1980;34(2):292–305. doi: 10.2307/2407393. - DOI - PubMed
    1. Hedrick AV, Temeles EJ. The evolution of sexual dimorphism in animals: hypotheses and tests. Trends Ecol Evol. 1989;4(5):136–138. doi: 10.1016/0169-5347(89)90212-7. - DOI - PubMed
    1. Rice WR. Sex chromosomes and the evolution of sexual dimorphism. Evolution; Int J Organic Evolution. 1984;38(4):735–742. doi: 10.2307/2408385. - DOI - PubMed
    1. Rhen T. Sex-limited mutations and the evolution of sexual dimorphism. Evolution; Int J Organic Evolution. 2000;54(1):37–43. doi: 10.1111/j.0014-3820.2000.tb00005.x. - DOI - PubMed

LinkOut - more resources

Feedback