Monocyte Lineage Expansion Drives Transcriptomic Individuality in Genetically Identical Armadillo Quadruplets

Abstract

Genetic diversity shapes phenotypes, yet even genetically identical individuals differ. In nine-banded armadillo (Dasypus novemcinctus) quadruplets, we previously showed that allele-specific expression (ASE) imbalances provide a stable molecular fingerprint of individuality. Here, we test whether such transcriptomic individuality reflects functional biological differences. We profiled bulk blood RNA from five cohorts of genetically identical quadruplets across three time points, and found persistent gene-expression signatures that predict individual identity. Focusing on a highly variable cohort, we then performed single-cell RNA-seq and ATAC-seq. In this litter, the most stably distinct individual showed an expanded monocyte-lineage compartment and gene-expression programs enriched for inflammatory and differentiation pathways. These cell-type and regulatory differences were stable over time and robust to experimental leprosy infection. Together, our results link transcriptomic individuality to lasting differences in immune-cell composition, illustrating how early stochastic events can produce persistent, biologically meaningful divergence among genetically identical individuals.