Origin of small chromosome A08 and genome evolution of Arachis species

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. Genome evolutionary history of wild Arachis species remains unclear. Here, the authors report the origin of small chromosome A08 and genome evolution of Arachis species via comparative oligopainting and genomic analysis of A. hoehnei.