Large-scale RNAseq analysis reveals new insights into the key genes and regulatory networks of anthocyanin biosynthesis during development and stress in cassava

Abstract Anthocyanins play key roles in plant development and response to various biotic and abiotic stresses including drought, cold, and pathogens. However, the key genes and regulatory networks relevant to anthocyanin biosynthesis remain largely elusive in cassava (Manihot esculenta L.), an important starchy root crop in tropical and sub-tropical regions. In this study, 465 RNAseq data were gathered to construct gene coexpression networks in cassava, resulting in a total of 30 coexpression modules (M1-M30). The associations of module-tissue or module-stress/development were systematically analyzed. Meanwhile, the hub genes and molecular roles were extensively dissected for each module, respectively. Notably, module M5 was significantly enriched in phenylpropanoid and flavonoid metabolisms, and several crucial genes participating in anthocyanin biosynthesis were included, suggesting a major role of M5 in anthocyanin biosynthesis in cassava. Coexpression analyses further revealed that phenylalanine ammonia-lyase 1 (PAL1), anthocyanidin synthase (ANS), and flavanone 3-hydroxylase (F3H) were the hub genes with most connections to others. Four transcription factors and three cis-regulatory motifs which might involve in anthocyanin biosynthesis regulation were also explored. Finally, a conserved coexpression network, covering the entire pathway of anthocyanin biosynthesis, was revealed among cassava, Arabidopsis thaliana (L.), and rice (Oryza sativa L.). The results provide valuable information to the key genes and regulatory networks of anthocyanin biosynthesis, and also lay a useful foundation for the genetic improvement in cassava.