Unravelling the Gondwanan Genome of Macadamia

Macadamia is a nut crop derived primarily from the Australian subtropical rainforest tree species Macadamia integrifolia. Macadamia is the only member of Australia’s flora to have been developed as a major international food crop. It belongs to the ancient angiosperm plant family Proteaceae, which is thought to have diverged from its closest extant relatives over 100 million years ago. Little is known of the composition and organisation of the Proteaceae genome. Although high throughput and low sequencing costs have facilitated assembly and annotation of a large number of species in various families, the Proteaceae has been largely neglected, and to our knowledge no other genome from this family has yet been sequenced.

We have generated more than 50GB (~64X) of usable data (both paired-end and mate-pair sequencing reads) using Illumina GAII and HiSeq platforms from a widely grown Macadamia integrifolia cultivar, 741. K-mer based estimation reveals the genome size to be approximately 780 megabases. Several state of the art de-bruijn graph based assemblers have been employed to assemble the genome. The best draft assembly, estimated to cover ~80% of the genome, is produced by the CLC de-novo assembler, with 193,493 scaffolds and an N50 of 4.7kb.  The draft assembly has a relatively low repetitive DNA content of 30%. The Maker gene annotation pipeline predicted 29,086 high confidence gene models with ~77% identity to Arabidopsis genes. These data provides opportunities to identify genes associated with specific traits of importance to the macadamia industry and will inform further evolutionary studies across the Proteaceae.