A comprehensive single-cell atlas of monoallelic expression across various tissues in zebrafish

Monoallelic expression (MAE), the preferential transcription of one allele in diploid organisms, plays a crucial role in generating cellular heterogeneity and phenotypic diversity. Although MAE has been extensively characterized in humans and mice, previous studies have been limited by clonal analyses or insufficient cell-type resolution, leaving its dynamics during development largely unexplored. In this study, we present a comprehensive single-cell atlas of allelic expression in zebrafish, leveraging reciprocal crosses between divergent strains, whole-genome sequencing, and single-cell RNA sequencing at two developmental stages. Using maximum likelihood estimation, we profile allele-specific expression patterns across 50,819 cells and 37 distinct cell types, identifying 738 genes (16.5% of evaluable genes) with MAE. MAE SNVs exhibit chromosomal clustering and regional enrichment, and MAE genes show functional specialization, being enriched in chromatin remodeling and hematopoietic processes. Notably, MAE genes are more likely to be tissue-specific markers, particularly in the epidermis, periderm, and erythrocytes. Tissue context further shapes allele choice, with distinct allelic biases observed in specific cell types. Together, our findings provide a comprehensive single-cell atlas of allelic expression in zebrafish, revealing the widespread and dynamic nature of MAE during vertebrate development and its contribution to tissue specialization and regulatory diversity.