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.
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BibTeX
@article{yang2026telomeretotelomere,
title = {{Telomere-to-telomere genome of a dodecaploid desert shrub Prunus pedunculata reveals polyploidy-driven arid adaptation}},
author = {Qian Yang and Junpeng Ma and Junru Wang and Xia Yang and Siyu Xie and Long Wang and Wenqun Fei and Wandong Yang and Mengxi Huang and Liang Zhao},
journal = {Genome Biology},
year = {2026},
month = oct,
doi = {10.1186/s13059-026-04317-2},
url = {https://link.springer.com/article/10.1186/s13059-026-04317-2},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Telomere-to-telomere genome of a dodecaploid desert shrub Prunus pedunculata reveals polyploidy-driven arid adaptation
AU - Qian Yang
AU - Junpeng Ma
AU - Junru Wang
AU - Xia Yang
AU - Siyu Xie
AU - Long Wang
AU - Wenqun Fei
AU - Wandong Yang
AU - Mengxi Huang
AU - Liang Zhao
PY - 2026
DA - 2026/10/29
JO - Genome Biology
DO - 10.1186/s13059-026-04317-2
UR - https://link.springer.com/article/10.1186/s13059-026-04317-2
AB - 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.
SN - 1474-760X
ER -