Many species from across the vascular plant tree-of-life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs). Bomarea multiflora (Alstroemeriaceae) is a tropical climbing monocot with unique underground morphology, including tuberous roots. We take a comparative transcriptomics approach to characterizing the molecular mechanisms of tuberous root formation in B. multiflora and compare these mechanisms to those identified in other underground storage structures across diverse plant lineages. We sequenced transcriptomes from the growing tip of four tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of three individuals of B. multiflora. We identify differentially expressed isoforms and test the expression of candidate genes that have been implicated in underground storage in other taxa. We identify 271 genes that are differentially expressed in root tubers versus fibrous roots, including genes implicated in cell wall modification, environmental signaling and flowering time, and starch biosynthesis. We also identify a phosphatidylethanolamine-binding protein (PEBP) that is over-expressed in tuberous roots. These findings demonstrate that deeply parallel processes underlie the formation of underground storage structures despite long evolutionary distances between taxa and non-homologous morphologies, illustrating that repeated co-option of similar genetic pathways can lead to convergent morphologies.

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation.