The genomes of the Macadamia genus

Abstract

Macadamia, a genus native to Eastern Australia, comprises four species, Macadamia integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii. Macadamia was recently domesticated largely from a limited gene pool of Hawaiian germplasm and has become a commercially significant nut crop. Disease susceptibility and climate adaptability challenges, highlight the need for use of a wider range of genetic resources for macadamia production. High quality haploid resolved genome assemblies were generated using HiFiasm to allow comparison of the genomes of the four species. Assembly sizes ranged from 735 Mb to 795 Mb and N50 from 53.7 Mb to 56 Mb, indicating high assembly continuity with most of the chromosomes covered telomere to telomere. Repeat analysis revealed that approximately 61% of the genomes were repetitive sequence. The BUSCO completeness scores ranged from 95.0% to 98.9%, confirming good coverage of the genomes. Gene prediction identified 37198 to 40534 genes. The ks distribution plot of Macadamia and Telopea suggests Macadamia has undergone a whole genome duplication event prior to divergence of the four species and that Telopea genome was duplicated more recently. Synteny analysis revealed a high conservation and similarity of the genome structure in all four species. Differences in the content of genes of fatty acid and cyanogenic glycoside biosynthesis were found between the species. An antimicrobial gene with a conserved cysteine motif was found in all four species. The four genomes provide reference genomes for exploring genetic variation across the genus in wild and domesticated germplasm to support plant breeding.