Highly dynamic, coordinated, and stage-specific profiles revealed by multi-omics integrative analysis during cassava tuberous root development

Cassava is an important starchy root crop providing food for millions of people worldwide, however, less is known about the regulation of cassava tuberous root development at multi-omics levels. Herein, transcriptome, proteome, and metabolome were parallelly performed to investigate the development of cassava tuberous roots from seven time-points, corresponding to the early-, middle-, and late-stage in production. Overall, genes/proteins exhibited highly dynamic and stage-specific expression changes during tuberous root development. Cell wall and auxin genes, which were regulated exclusively at the transcriptomic level, mainly functioned at the early-stage. Starch biosynthesis, which was controlled at both transcriptomic and proteomic levels, was mainly activated at the early-stage but greatly restricted at the late-stage. Two main branches, coniferyl alcohol and sinapyl alcohol, of lignin biosynthesis also functioned at the early-stage at both transcriptomic and proteomic levels. Metabolomic analysis further supported the stage-specific roles of genes/proteins. Metabolites related to lignin and flavonoid biosynthesis showed high abundance at the early-stage, those related to lipids exhibited high abundance at the early- and mid-stage, while those related to amino acids were highly accumulated at the late-stage. These findings provide a comprehensive resource to broaden our understanding of tuberous root development and facilitate cassava genetic improvement.