Elucidating the unknown transcriptional responses and PHR1 mediated biotic and abiotic stress tolerance during phosphorus-limitation

Phosphorus (P) limitation in the majority of world soils is a major constraint for plant growth and crop productivity. RNA sequencing was used to discover novel P-responsive gene transcripts (PRGT) in leaves and roots of Arabidopsis. Hisat StringTie and Cufflinks TopHat transcript assembler were used to analyze reads and identify 1,074 PRGTs with a >5-fold altered abundance during P-limitation. Interestingly, 60% of these transcripts were not previously reported. Among the novel PRGT, 106 were from unannotated genes, and some were among the most P-responsive, including At2g36727 which encodes a novel microRNA. Annotated novel PRGTs encode for transcription factors, microRNAs, small signaling peptides, long non-coding RNAs, defense-related proteins, and transporters, along with proteins involved in many biological processes. We identified several genes that undergo alternative splicing during P-limitation, including a novel miR399 resistant splice variant of PHOSPHATE2 ( PHO2 . 2 ). Several novel P-responsive genes were regulated by PHOSPHATE STARVATION RESPONSE1 ( PHR1 ), PHR1-LIKE 1 ( PHL1 ) and PHO2 . We discovered that P-limited plants show increased resistance to pathogens and drought stress mediated by PHR1-PHL1. Identification of novel P-responsive transcripts and the discovery of the influence of P-limitation on biotic and abiotic stress adds a significant component to our understanding of plant P-signaling. Highlight Phosphorus limitation elicits the expression of several novel genes including many previously unannotated genes, noncoding RNAs, small peptides and alternatively spliced RNAs, and leads to enhanced disease and drought tolerance.