Figure 4.

Transcriptome Characteristics of Zebrafish Gonads with Partially Depleted and WT PGCs Demonstrate the Divergence of WT Individuals and Clustering between WT and PGC-Depleted Transforming Males at Different Developmental Stages

(A) At 14 dpf, the PCA plot showed that PGC-depleted samples (1–9; cluster 1, red) did not group closely with WT samples (clusters 2 and 3, blue and green, respectively).

(B) The heatmap of hierarchical clustering of 132 DE genes at 14 dpf between PGC-depleted and WT (>2-fold, p < 0.05) showed cluster 1 separated from clusters 2 and 3.

(C) At 22 dpf, the PCA plot showed several distinct clusters, suggesting the high variability in the transformation process from females to males. Cluster 1 was assigned as immature female. Clusters 2, 3, and 4 were assigned as transforming gonads from female to male, and cluster 5 was assigned as PGC-depleted transforming male.

(D) The heatmap produced by hierarchical clustering of 1,329 genes that showed differential expression at 22 dpf when cluster 1 was compared with clusters 4 and 5 (>2-fold, p < 0.05). As shown, cluster 4 was grouped with cluster 5 (PGC-depleted male); cluster 3 displayed a transitional pattern and was closer to cluster 5.

See also Table S2 for a list of gene symbols and names, Table S3 for a list of DE genes, and Table S4 for functional classification of DE genes.