Parallel_single_cell_genome_and_transcriptome_sequencing_reveals_allele_specific_expression_in_zebrafish_spermatids

Genetic and phenotypic variation among sperm produced by a single male provides a unique opportunity for efficient selection at the post-meiotic haploid stage. Cytoplasmic bridges connecting developing spermatids have long been thought to ensure that post-meiotic cells remain functionally diploid and prevent genetic conflict such as meiotic drive systems. However, cytoplasmic sharing may be incomplete, allowing allele-specific expression based on the underlying haplotypes to persist in post-meiotic cells. Here, we performed parallel single-cell genome and transcriptome sequencing in haploid spermatids in the zebrafish Danio rerio to directly link cellular transcripts with their underlying haploid genotypes. We used transcriptome profiles to carefully stage individual cells developmentally and confirm the timing of gene expression as spermatids mature. Transcriptional activity remained substantial, with ~1100 genes expressed in early round spermatids and ~600 genes in late elongated spermatids, reflecting a gradual decline in gene expression as spermatids mature. While 94% of genes exhibited complete sharing, approximately 4% showed partial sharing, and 2% showed no evidence of transcript sharing. Notably, genes with incomplete or absent sharing were enriched for roles in cell division and apoptosis – processes playing a key role during spermatogenesis and embryo development. Our findings provide direct evidence for allele-specific gene expression and support the idea of haploid selection acting in sperm directly contributing to inheritance patterns across generations.