Single-Nucleus Transcriptomics Identifies Stage-Associated Differences in the Olfactory Epithelium During Natural Sex...

The rice field eel (Monopterus albus) undergoes natural protogynous sex reversal, but whether peripheral sensory tissues differ across sexual stages remains poorly understood. We used single-nucleus RNA sequencing to characterize the olfactory epithelium (OE) of female, intersex, and male rice field eels. After quality control, 22,959 nuclei were retained and classified into 19 cell populations, including olfactory sensory neurons (OSNs), basal/progenitor, epithelial, mesenchymal, endothelial, and immune populations. OE tissues from five individuals within each sexual stage were pooled prior to nuclei isolation, resulting in one pooled snRNA-Seq library per stage; therefore, between-stage comparisons are interpreted as exploratory and descriptive rather than as independently replicated population-level differences. The relative representation of captured nuclei differed among stages, particularly within the sensory neuronal and basal-cell compartments. Pseudotime analysis placed immature OSNs at relatively early transcriptional states associated with ciliated and microvillous OSN populations, whereas CrOSNs were not continuously connected to the principal iOSN-cOSN/mOSN trajectory. Cell-type-specific analyses identified stage-associated transcriptional differences in basal cells and multiple OSN populations. Predicted cell-cell communication profiles also differed among stages, with male OE showing a larger nominal number of inferred interactions but lower overall predicted interaction strength. Expression patterns of ompa, gng8, and ora4 supported the marker-based annotation of major OSN populations within the dataset. These findings provide an exploratory single-nucleus framework for investigating stage-associated variation in the peripheral olfactory system of M. albus.