The origin of the small chromosome 8A and genome evolution of Arachis species

Wild Arachis species exhibit abundant genetic diversity for peanut improvement. However, their genome evolutionary history remains unclear. Here, we show that comparative oligopainting corresponds all actual chromosomes to the pseudomolecules of Arachis duranensis, A. ipaensis, and cultivated peanut, and determines ten homoeologous groups (Hgs) of A, B, F, K, and H genome chromosomes. Chromosomes in Hg1, Hg3 and Hg4 are highly conserved, while those in Hg2, and Hg5–Hg10 exhibit significant variations. A T2T genome assembly of A. hoehnei, discovers its genome identity as A'. The unique small chromosome 8A originates from two inversions and one substantial contraction of 8A'. A genome evolution model of the Arachis genus is thus proposed, where A' bridges the B and A genomes. We also report an artificial hexaploid derived from cultivated peanut and A. hoehnei, and four candidate genes involved in web-blotch resistance in A. hoehnei, which are valuable for peanut breeding.