Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-Bipolaris sorghicola interaction

Seventy-six-base-pair reads from mRNAs of mock- or pathogen-infected leaves were sequenced. Unannotated transcripts were predicted on the basis of the piling-up of mapped short reads. Differentially expressed genes were identified statistically; particular genes in tandemly duplicated putative paralogs were highly upregulated. Pathogen infection activated the glyoxylate shunt in the TCA cycle; this changes the role of the TCA cycle from energy production to synthesis of cell components. The secondary metabolic pathways of phytoalexin synthesis and of sulfur-dependent detoxification were activated by upregulation of the genes encoding amino acid metabolizing enzymes located at the branch point between primary and secondary metabolism. Coordinated gene expression could guide the metabolic pathway for accumulation of the sorghum-specific phytochemicals 3-deoxyanthocyanidin and dhurrin. Key enzymes for synthesizing these sorghum-specific phytochemicals were not found in the corresponding region of the rice genome.Pathogen infection dramatically changed the expression of particular paralogs that putatively encode enzymes involved in the sorghum-specific metabolic network.Plants synthesize low-molecular-weight phytoalexins via secondary metabolic pathways to protect themselves from pathogens such as fungi [1]. Phytoalexins of sorghum such as 3-deoxyanthocyanidins first appear in the cells under fungal attack, where they accumulate in cytoplasmic inclusion bodies. The inclusions migrate to the site of attempted penetration, become pigmented, and ultimately release phytoalexins to kill the fungus [2]. Phytoalexins are produced mainly from aromatic amino acids (phenylalanine (Phe), tyrosine (Tyr)) by the action of many enzymes that sequentially catalyze biochemical reactions. Phenylalanine ammonia lyase (PAL) catalyzes the deamination of Phe to trans-cinnamic acid; this is the first step in the biosynthesis of various phenylpropanoids, coumarins, flavonoids, and lignin [3-5]