Marsupial single-cell transcriptomics identifies temporal diversity in mammalian developmental programmes

Single-cell transcriptomics has demonstrated conserved and divergent programmes of organogenesis in mammals, but existing studies have focused on eutherians. Marsupials exhibit short gestation and complete development externally, necessitating accelerated differentiation of anterior features required for locomotion and feeding. Hence, they represent a unique outgroup for studying temporal shifts in development, known as heterochrony. Here, we generate a single-cell transcriptomic atlas of gastrulation and early organogenesis in a marsupial, the opossum Monodelphis domestica. We identify previously undocumented tissues undergoing heterochrony, and find that transcriptional programmes that form anterior structures initiate earlier and progress faster relative to eutherians. The result is uncoupling of transcriptional and morphological timelines, revealing unforeseen diversity in mammalian developmental sequences. Using our transcriptomic dataset, we identified translation as a candidate control mechanism by which anterior prioritisation is achieved. Our findings provide insight into the asynchronous progression of developmental programmes in marsupials. Overall design: Opossum (Monodelphis domestica) embryos at four time points encompassing gastrulation and early organogenesis were processed for single-cell RNA-sequencing