Comparative analysis of Xenopus mesonephric transcriptomics: Conservation of the developmental lineage of nephron stages

The vertebrate kidney develops through three sequential forms: the pronephros, mesonephros, and metanephros. These three forms are composed of segmented nephrons that mediate fluid filtration and solute homeostasis. In aquatic egg-laying vertebrates such as Xenopus laevis, the mesonephros serves as the final functional renal organ, whereas in mammals it is a transient embryonic structure that precedes metanephric development. Despite its central developmental and evolutionary significance, the cellular and transcriptional organization of the mesonephric kidney remains poorly defined at single-cell resolution. Here, we mapped the cellular and transcriptional landscape of the Xenopus laevis mesonephros from NF stages 46-53 to define its composition and analyze its relationship to other kidney types. By integrating single-cell RNA sequencing with in situ hybridization, immunostaining, and functional uptake assays, we identify mesonephric nephron segments, progenitor populations, and the progressive transition from mesenchymal precursors to differentiated epithelial tubules. Transcriptomic profiling of 14,411 cells reveals conserved nephron segment identities and shared differentiation programs revealed conserved nephron segment identities and a clear transition from mesenchymal progenitors to epithelialized tubules. Comparative analyses with published Xenopus pronephric and mammalian metanephric datasets identified strong transcriptional conservation between Xenopus mesonephric and mammalian metanephric nephrons. Functional assays confirmed the timing of filtrate uptake, marking the onset of renal function during metamorphosis. Together, these findings provide the first comprehensive single-cell map of Xenopus mesonephric development, demonstrating that the mechanisms of nephron patterning and differentiation are conserved across vertebrate kidney forms. This work establishes the Xenopus mesonephros as a robust model for studying vertebrate kidney development and evolutionary transitions among nephron types.