Comparative Transcriptomics ofArabidopsis,Medicago,BrachypodiumandSetariaspecies during Phosphorus limitation

Abstract

ABSTRACTTranslating biological knowledge fromArabidopsisto crop species is important to advance agriculture and secure food production in the face of dwindling fertilizer resources, biotic and abiotic stresses. However, it is often not trivial to identify functional homologs (orthologs) ofArabidopsisgenes in crops. Combining sequence and expression data can improve the correct prediction of orthologs. Here, we conducted a large-scale RNA sequencing based transcriptomics study ofArabidopsis,Medicago,BrachypodiumandSetariagrown side-by-side in Phosphorus (P)-sufficient and P-limited conditions to generate comparable transcriptomics datasets. Comparison of top 200 P-limitation induced genes inArabidopsisrevealed 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 P-starvation response were found conserved in all four species. This study reveals many known, novel, unannotated, conserved and species-specific regulations of the transcriptional P-starvation response. Identification and experimental verification of expressologs by independent RT-qPCR for P-limitation marker genes inPrunusshowed the usefulness of comparative transcriptomics in pinpointing the functional orthologs in diverse crop species. This study provides an unprecedented resource for functional genomics and translational research to create P-efficient crops.HIGHLIGHTComparative transcriptomics reveals novel, known, conserved and specific transcriptome responding to Phosphorus limitation inArabidopsis, Medicago, BrachypodiumandSetariato facilitate translational research in crops.