Amphicarpic development in the emerging model organism Cardamine chenopodiifolia

O_LIAmphicarpy is an unusual trait where two fruit types develop: one above and the other below ground. This trait is not found in conventional model species, therefore, its development and molecular genetics remain under-studied. Here, we establish Cardamine chenopodiifolia as an emerging experimental system to study amphicarpy. C_LIO_LIWe characterized the development of C. chenopodiifolia, focusing on differences in morphology and cell wall histochemistry between above- and below-ground fruit. We generated a reference transcriptome using PacBio full-length transcript sequencing (IsoSeq) and used a combination of short and long read sequencing to analyse differential gene expression between above- and below-ground fruit valves. C_LIO_LIC. chenopodiifolia has two contrasting modes of seed dispersal. The main shoot fails to bolt and initiates floral primordia that bury underground where they self-pollinate and set seed. By contrast, axillary shoots bolt to position flowers and exploding seed pods above ground. Morphological differences between aerial explosive fruit and subterranean non-explosive fruit were reflected in a large number of differentially regulated genes involved in photosynthesis, secondary cell wall formation and defence responses. C_LIO_LITools established in C. chenopodiifolia, such as a reference transcriptome, draft genome assembly and stable plant transformation, pave the way to explore under-studied traits and discover new biological mechanisms. C_LI