Fig. 1.

Testis vs ovary differential gene expression. a) Testis vs ovary differential expression plotted against genomic position across the 25 zebrafish chromosomes. The plot shows unique and specific upregulation of testis genes vs ovary genes on Chr4, the sex chromosome. b) Testis vs ovary differential expression across Chr4. The plot identified 4 distinct regions: R1, with values similar to the bulk of the genome; R2, with testis expression on average much higher than ovary expression; R3, again with values similar to most of the genome; and R4, with some strongly ovary-biased genes and coincident with sar4 containing the major sex-determining locus. The horizontal black bar represents Chr4, with the location of the centromere (horizontal red line) located by alignment of the centromeric markers BX537156 (Freeman et al. 2007) and Z20450 (Mohideen et al. 2000) to GRCz11; the positions of maternal 5S ribosomal genes (Locati, Pagano, Ensink et al. 2017) are indicated by green vertical lines, and mir430 genes are marked by white vertical lines. c) Replication banding of Chr4 and Chr3 (Amores and Postlethwait 1999; Phillips et al. 2006). Karyotypes showed dark staining (early replicating DNA) on the short (left) arm of Chr4 and at the distal tip of the long (right) arm of Chr4, in contrast to pale staining (late-replicating DNA) in the position expected for R2 on Chr4R, while only thin light bands appeared on all other chromosomes, represented here by Chr3. d) The absolute level of gene expression in transcripts per kilobase of gene length per million total reads (TPM) for all protein-coding genes within Region-2 of Chr4, showing that transcripts were detected from most genes in testis (blue) but transcript count was near 0 from most genes in ovary (red).