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Phosphorus (P) is an essential macronutrient for all organisms. Phosphate (Pi) deficiency reduces grain yield and quality in wheat. Understanding how wheat responds to Pi deficiency at the global transcriptional level remains limited. We revisited the available RNA-seq transcriptome from Pi-starved wheat roots and shoots subjected to Pi starvation. Genome-wide transcriptome resetting was observed under Pi starvation, with a total of 917 and 2338 genes being differentially expressed in roots and shoots, respectively. Chromosomal distribution analysis of the gene triplets and differentially expressed genes (DEGs) revealed that the D genome displayed genome induction bias and, specifically, the chromosome 2D might be a key contributor to Pi-limiting triggered gene expression response. Alterations in multiple metabolic pathways pertaining to secondary metabolites, transcription factors and Pi uptake-related genes were evidenced. This study provides genomic insight and the dynamic landscape of the transcriptional changes contributing to the hexaploid wheat during Pi starvation. The outcomes of this study and the follow-up experiments have the potential to assist the development of Pi-efficient wheat cultivars.