Genome-wide characterization of the PHT gene family in Uncaria rhynchophylla identified UrPHT1;11 as a key regulator to low phosphorus response

The soil available phosphorus (P) content in the karst regions of Southwest China is extremely low, yet Uncaria rhynchophylla, an important medicinal plant, is highly adaptable to such environments. This study aimed to elucidate the physiological and molecular mechanisms underlying the low-phosphorus (LP) response in U. rhynchophylla. Hydroponic experiments revealed that moderate LP (0.01mM Pi) significantly promoted lateral root formation, increased mesophyll tissue thickness, and increased the accumulation of chlorophyll and the major alkaloids. LP also improved the antioxidant capacity by increasing peroxidase (POD) activity and reducing malondialdehyde (MDA) levels. Genome-wide analysis revealed 58 phosphate transporter (PHT) genes distributed on 18 chromosomes and classified into five subfamilies (PHT1–PHT3, PHT5, and PHO). These genes exhibited strong structural conservation, with 27 segmentally duplicated gene pairs. Promoter analysis revealed abundant stress- and hormone-responsive cis -elements, particularly MYB (myeloblastosis)-binding motifs. Transcriptome analysis identified UrPHT1;11 as a strongly LP-induced gene, which was confirmed by quantitative real-time PCR (qRT‒PCR). Moreover, we discovered that the transcription factor UrMYB62 directly binds to and activates the UrPHT1;11 promoter. Our study provides insights into the evolution, expression, and regulation of the PHT family in U. rhynchophylla under phosphate limitation, advancing our understanding of the molecular mechanisms underlying its low phosphorus adaptation.