Abstract
Wild Arachis species exhibit abundant genetic diversity for peanut improvement. However, the evolutionary history of their genomes is unclear. Here, through comparative oligopainting, we establish a one-to-one correspondence between microscopically observed chromosomes and sequenced pseudomolecules of Arachis duranensis, A. ipaensis, and cultivated peanut, and determine the 10 homoeologous groups (Hgs) of the A, B, F, K, and H genomes. Analysis of the telomere-to-telomere (T2T) genome assembly of A. hoehnei reveals that its genome is a diverging form of the A genome and is designated as genome A’. In addition, the unique small chromosome A08 is originated from two inversions and a substantial contraction of A'08. We propose a genome evolution model of the Arachis genus, where A’ bridges the A and B genomes. We further report an artificial hexaploid peanut derived from a hybrid of cultivated peanut and A. hoehnei, and identify differentially expressed genes against web blotch in A. hoehnei.
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Data availability
The raw data of genome sequencing of Arachis hoehnei (Zw61), genome resequencing data and transcriptome sequencing data were deposited in the National Center for Biotechnology Information under accession PRJNA605106. The telomere-to-telomere (T2T) genome assembly, gene annotations, and chloroplast genomes of A. hoehnei (Zw61) were available at Zenodo [https://doi.org/10.5281/zenodo.18161068]. Additionally, data on chromosomes, agronomic traits data, and sequences of 10 chromosome-specific single copy oligonucleotide libraries (CSCOLs) can be accessed at Zenodo [https://doi.org/10.5281/zenodo.18168257]. Source data are provided with this paper.
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Acknowledgements
We thank Yonghua Han (Jiangsu Normal University, Xuzhou, China) for help in designing and labeling the oligonucleotide libraries. We thank Robert McIntosh, University of Sydney, Australia, for his kind review, suggestions, and language editing. We are also grateful to Dawn M. Schmidt (www.editbydawn.com) for English editing. This project is supported by Henan Province Science and Technology R&D Joint Fund (232301420025 to P.D.), National Natural Science Foundation of China (32272153 to P.D. and 32501918 to L.F.), the Key Research Project of the Shennong Laboratory (SN01-2022-03 to X.Z.), China Agriculture Research System (CARS-13 to X.Z.), Henan Provincial Agriculture Research System (S2012-5 to W.D.), and innovation team of peanut breeding (2024TD01 to X.Z.). The funding agencies played no role in the design of the study and collection, analysis, and interpretation of data or in writing the manuscript.
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X.Z., Z.Q. and P.D. designed and supervised the project. P.D., L.F., G.C., Q.W., C.L., Zhiyuan Z., and L.M. performed the experiments. S.H., X.W., Z.S., Zhiyuan Z., X.X., H.L., L.Q., J.X. and Zhongxin Z. analyzed the data. P.D., G.C. and L.F. wrote the manuscript. X.Z., Z.Q., W.D., and Zheng Z. provided critical guidance for the revision of the manuscript.
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Du, P., Fu, L., Chen, G. et al. Origin of small chromosome A08 and genome evolution of Arachis species. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68884-5
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DOI: https://doi.org/10.1038/s41467-026-68884-5
