Comparative Transcriptomics of Arabidopsis, Brachypodium, Medicago and Setaria species Pinpoints Conserved and Specific Transcriptional Responses to Phosphorus Limitation

Translating biological knowledge from Arabidopsis to legume and grass crop species is important to advance agriculture and secure food production in the face of dwindling fertilizer resources, climate change, biotic and abiotic stresses. However, it is often not trivial to identify functional homologs (orthologs) of Arabidopsis genes in crop species. Combining sequence and expression data can improve the correct prediction of orthologs. Here, we conducted a large RNA-Seq transcriptomics study of Arabidopsis, Medicago, Brachypodium and Setaria grown side-by-side in P-limited and P-sufficient conditions to gain insights into orthologous relationships of phosphorus (P) status-responsive genes. Known, conserved, and novel P-responsive genes were identified in the four species. Comparison of the top 200 P starvation-inducible genes in Arabidopsis revealed that ~80% of these genes have identifiable close homologs in the other three species but only ~50% retain their P-limitation response in the legume and grasses. Most of the hallmark genes of the phosphate starvation response were found conserved in all four species. The results show the usefulness of comparative transcriptomics for pinpointing orthologous genes across species and reveal considerable species-specific regulation of the transcriptional P-starvation response. Identification and experimental verification of expressologs by independent RT-qPCR for P-limitation marker genes in Prunus showed the usefulness of comparative transcriptomics in pinpointing the functional orthologs in diverse crop species. The study provides an unprecedented insight into conserved and species-specific P-limitation responses and a resource for functional genomics, applied and translational research for Arabidopsis, legumes, grasses, and tree species.