Telomere-to-telomere genome of a dodecaploid desert shrub Prunus pedunculata reveals polyploidy-driven arid adaptation

Abstract Background Geographical imbalance in extremophile plant genomics has left the Mongolian Plateau underexplored. Prunus pedunculata , a desert shrub endemic to this arid region, provides an ideal system for understanding woody plant adaptation to extreme drought, yet its genomic architecture remains unknown. Results Here we present a telomere-to-telomere genome assembly for P. pedunculata , a dodecaploid (2n = 12 × = 96) with the highest ploidy level among sequenced woody perennials. Its 1.38 Gb genome is resolved into 48 chromosomes, and telomeric repeats are detected in each. Evolutionary analysis confirms an autopolyploid origin with > 80% subgenome consistency and no evidence of hybridization. The most recent whole-genome duplication dates to approximately 3.49 million years ago, coinciding with the uplift of the Tibetan Plateau and the intensification of Asian interior aridity. Ancestral karyotype reconstruction using six Prunus species spanning diploid to dodecaploid genomes and three inflorescence types reveals an eight chromosome ancestor and post polyploidization chromosomal rearrangements. Organ specific transcriptomics under progressive drought uncovers a coordinated division of labor that integrates ABA, CLE25 , BES1 / BIN2 , and auxin signaling modules to orchestrate growth cessation and stress survival. Drought induced genes significantly overlap with expanded gene families, demonstrating functional recruitment of polyploidy derived redundancy. Conclusions This work confirms an autopolyploid origin for P. pedunculata and links this polyploidization event to the aridification of the Asian interior. Duplicated genes have been repurposed for drought stress, and a multi-component signaling network coordinates organ responses and enhances survival under water scarcity, offering leads for crop improvement.