Selected genomic features within differentially replicating regions. (A) Scatterplot of the GSC-like (x-axis) and CySC-like (y-axis) replication timing values for genes located within the pericentromeric region of Chromosome 2L. Each data point represents a gene, in which each gene is colored by its log₂FE value calculated by differential gene expression analysis of our scRNA-seq (Supplemental Table S2). Green represents transcript enrichment (log₂FE) in GSC-like cells, whereas purple indicates enrichment in CySC-like cells. (B) A genome-browser image of the pericentromeric region of Chromosome 2L. In green are the replication timing tracks for GSC-like cells, in which the replication timing tracks for CySC-like cells are in magenta. Shown highlighted are the genes found to have differential replication timing and gene expression in GSC-like cells (blue arrows are protein-coding genes, and orange bars are noncoding RNAs). Also indicated is the location of Orc2 binding sites, which represent putative origins of replication. (C,D) Scatterplots of the GSC-like (x-axis) and CySC-like (y-axis) replication timing values for genes located on the X Chromosome, separated by whether they replicate earlier in GSC-like or CySC-like cells. Each data point represents a gene, in which each gene is colored by its log₂FE value, which is calculated using differential gene expression analysis of the scRNA-seq (Supplemental Table S2). Green represents transcript enrichment in GSC-like cells, whereas purple indicates enrichment in CySC-like cells. (E,F) Shown is the proportion of gene types that replicate earlier in GSC-like or CySC-like cells. The majority are protein-coding genes, and the next largest gene category is long noncoding RNAs. (G) A genome-browser image of the fourth chromosome with one 64 kb region highlighted that is earlier replicating in GSC-like cells. The replication timing tracks for GSC-like cells are in green, and the replication timing tracks for CySC-like are magenta. Shown is the location of six tandem genes (protein coding in blue) residing in this earlier replicating domain, including a noncoding RNA (in orange) and Orc2 binding site. (H) Scatterplot of the GSC-like (x-axis) and CySC-like (y-axis) replication timing values for genes located on the fourth chromosome. Each data point represents a gene. Genes present within the 64 kb region cluster together as earlier replicating in GSC-like cells. (I) Scatterplot of the GSC-like (x-axis) and CySC-like (y-axis) replication timing values for genes located on the Y Chromosome. Each data point represents a gene. Genes that replicate earlier in CySC-like cells with potential roles in male fertility are indicated as marked.