The genome of the endangeredMacadamia janseniidisplays little diversity but represents an important genetic resource for plant breeding

Abstract

Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.

The genomes of theMacadamiagenus

“…Heterozygosity between the haplotypes in diploids can complicate the genome assemblies. The low heterozygosity of M. jasnenii and high heterozygosity of M. integrifolia and M. tetraphylla (Sharma et al, 2021b;Xia et al, 2022;Nock et al, 2020b;Niu et al, 2022) was also supported by k-mer analysis, haploid assembly statistics and dotplot comparisons. The dotplot comparison of the two M. jansenii haploid assemblies, showing minimal differences between the two.…”

“…The comparison of genome assemblies of the already available genomes of M. jansenii, M. integrifolia, and M. tetraphylla with those generated in this study revealed notable improvements in the assembly statistics. For M. jansenii, the newly assembled genome demonstrated an increase in length (from 758Mb to 773Mb), improvement in N50 value from 52Mb to 55Mb and slight improvement in BUSCO as compared to the already available M. jansenii Hi-C assembly's 758 Mb (Sharma et al, 2021b). This study has greatly improved the M. integrifolia (cultivar 741) genome with a longer assembly length of 775 Mb and a significantly higher BUSCO of 97% and N50 value of 53 Mb as compared to previous assemblies by Nock et al, in 2016 (N50: 4.7 kb) & 2020 (N50: 413 kb) (Nock et al, 2016;Nock et al, 2020b).…”

“…The HiFi sequencing data of the four Macadamia species (Sharma et al, 2021b) was used for this study. RNA sequence data for M. jansenii was used from Sharma et al, 2021a.…”