Sexual dimorphism in brain transcriptomes of Amami spiny rats (Tokudaia osimensis): a rodent species where males lack the Y chromosome

Fig. 1. PCA analysis. Three samples were obvious outliers: male sample #1, female sample #2 and female sample #3, and thus, these samples were removed from further RNAseq expression analysis

Fig. 2. Volcano plot analyses of differentially expressed genes. The volcano plot represents the relationship of each gene’s log2 fold change vs -log10 pvalue. Orange points represent expression ratios greater than 2X (either up or down), red points represent genes whose FDR-corrected p-values are < 0.05 and green points are genes where both properties occur (fold-change > +/− 2X and FDR < 0.05)

Fig. 3. Volcano plot analyses of differentially expressed transcripts. The volcano plot represents the relationship of each transcript’s log2 fold change vs -log10 pvalue. Orange points represent expression ratios greater than 2X (either up or down), red points represent transcripts whose FDR-corrected p-values are < 0.05 and green points are transcript where both properties occur (fold-change > +/− 2X and FDR < 0.05)

Fig. 4. STRING pathway analyses diagram for genes upregulated in males. Based on genes identified to be upregulated in males, two main clusters are identified with one cluster comprised of genes such as Myl1, Mb, Trdn, Myl2, Csrp3, and Smpx in the center. The second cluster includes Fmod, Omd, Ogn, Dcn, Col3a1, and Lum. Network nodes represent proteins. Splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus. Node colors are arbitrary. Edges represent protein-protein associations. Associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding each other. Edge confidence is the relative amount of supporting evidence for the connection between two proteins in the diagram. Thicker lines have more support; thinner lines have less support

Fig. 5. STRING pathway analyses diagram for transcripts upregulated in males. The primary group of transcripts upregulated in the brain of male Amami spiny rat are transcripts encoding zinc finger proteins (yellow highlighted area). Several other smaller clusters are present. Network nodes represent proteins. Splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus. Node colors are arbitrary. Edges represent protein-protein associations. Associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding each other. Edge confidence is the relative amount of supporting evidence for the connection between two proteins in the diagram. Thicker lines have more support; thinner lines have less support

Fig. 6. STRING pathway analyses diagram for transcripts upregulated in females. Based on the elevated transcripts, several pathways are affected in females. Examples include nucleotide, purine ribonucleoside, ribonucleotide, carbohydrate derivative, heterocyclic, zinc ion, ATP, transitional metal ion, cytoskeletal protein, GABA receptor binding pathways, hydrolase, nucleoside triphosphate, ATPase, L-amino acid transmembrane transporter, and palmitoyl-CoA 9-desaturase activity. Network nodes represent proteins. Splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus. Node colors are arbitrary. Edges represent protein-protein associations. Associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding each other. Edge confidence is the relative amount of supporting evidence for the connection between two proteins in the diagram. Thicker lines have more support; thinner lines have less support

Fig. 7. qPCR analyses for select genes in the brain of female and male Amami spiny rats. A) Svs expression. B) Cyp1b1. C) Serpina3n. *p = 0.0005. **p = 0.05