The Chromosome-Scale Reference Genome of Macadamia tetraphylla Provides Insights Into Fatty Acid Biosynthesis

Abstract

Macadamia is an evergreen tree belonging to the Proteaceae family. The two commercial macadamia species, Macadamia integrifolia and M. tetraphylla, are highly prized for their edible kernels. The M. integrifolia genome was recently sequenced, but the genome of M. tetraphylla has to date not been published, which limits the study of biological research and breeding in this species. This study reports a high-quality genome sequence of M. tetraphylla based on the Oxford Nanopore Technologies technology and high-throughput chromosome conformation capture techniques (Hi-C). An assembly of 750.87 Mb with 51.11 Mb N50 length was generated, close to the 740 and 758 Mb size estimates by flow cytometry and k-mer analysis, respectively. Genome annotation indicated that 61.42% of the genome is composed of repetitive sequences and 34.95% is composed of long terminal repeat retrotransposons. Up to 31,571 protein-coding genes were predicted, of which 92.59% were functionally annotated. The average gene length was 6,055 bp. Comparative genome analysis revealed that the gene families associated with defense response, lipid transport, steroid biosynthesis, triglyceride lipase activity, and fatty acid metabolism are expanded in the M. tetraphylla genome. The distribution of fourfold synonymous third-codon transversion showed a recent whole-genome duplication event in M. tetraphylla. Genomic and transcriptomic analysis identified 187 genes encoding 33 crucial oil biosynthesis enzymes, depicting a comprehensive map of macadamia lipid biosynthesis. Besides, the 55 identified WRKY genes exhibited preferential expression in root as compared to that in other tissues. The genome sequence of M. tetraphylla provides novel insights for breeding novel varieties and genetic improvement of agronomic traits.

The genomes of theMacadamiagenus

“…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). Similarly, the M. tetraphylla genome showed great improvement in terms of N50 56 Mb and 98% BUSCO as compared to already available M. tetraphylla genome (Niu et al, 2022). The genome assemblies generated in this study provide enhanced continuity, higher BUSCO completeness, and increased gene identification compared to previous versions, providing a robust basis for genome comparison.…”

“…A further update on the M. jansenii contig level assembly reported the possibility of achieving de novo assembly of near chromosome level from sequenced data alone, without using any scaffolding method (Sharma et al, 2022). Recently, a more contiguous and complete assembly of the M. integrifolia Chinese cultivar -GUIRE 1(GR1) (Xia et al, 2022) and the M. tetraphylla genome were also reported (Niu et al, 2022). The M. integrifolia (GR1) chromosome level genome was assembled using Nanopore sequencing, producing a genome of 807 Mb, with a scaffold N50 of 54.7 Mb and 95.7% BUSCO.…”

Genomic resources forMacadamia tetraphyllaand an examination of its historic use as a crop resource in Hawaii

“…For validation and annotation, the assembled sequence was compared to the KEGG and PFAM databases (Mistry et al, 2021;Ogata et al, 1998). Similar to a previous report (Niu et al, 2022), a total of 46,967 transcripts were called representing 34,444 unigenes and 12,523 isoforms. As expected, there was tissue specific expression of transcripts and pathways (FPKM > 10 Figure 1b, c).…”

Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics in Macadamia

“…Macadamia plants are diploid (2n = 28) ( Peace et al., 2003 ) and their genome size ranges from 758 to 896 megabase (Mb) ( Nock et al., 2020 ; Niu et al., 2022a ). In recent years, several de novo -assembled macadamia genomes have been reported, providing new insight for genetic breeding.…”

“…Recently, the genome of the cultivar HAES 344 was sequenced and assembled into 14 pseudochromosomes by the use of Illumina NovaSeq and PacBio Sequel II sequencing (5387 contigs, N50 = 281 kb, 794 Mb) ( Lin et al., 2022 ). A chromosome-scale genome assembly of M. tetraphylla has also been constructed from long-read Oxford Nanopore Technologies (ONT) sequencing data (1059 scaffolds, N50 = 51 Mb, 751 Mb) ( Niu et al., 2022a ). Moreover, in recent years, the chloroplast and mitochondrion genomes of M. integrifolia , M. tetraphylla , and M. ternifolia have been assembled and thoroughly annotated ( Niu et al., 2022b ).…”