The genome of the endangered Macadamia jansenii displays 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 52 Mb and a total genome assembly size of 758 Mb of which 56% is repetitive. Completeness assessment revealed that the assembly covered À97.1% 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.

De novo chromosome level assembly of a plant genome from long read sequence data

“…Dotplot analysis of a 159 Mb full length chloroplast genome assembled using the GetOrganelle toolkit (Jin et al., 2020 ) against the HiFiasm genome assembly indicated the insertion of small fragments of chloroplast sequences in the nuclear genome assembly (Figure 3a ; Figure S1A ), which also align with previously reported Hi‐C assembly results (Sharma et al., 2021b ) (Figure S1 B). Among the middle size contig set, only one contig (ptg0000186|) of 183 Mb aligned with the chloroplast genome (Figure 3b ).…”

“…A dotplot analysis of 14 pseudo‐molecules of M. jansenii Hi‐C assembly against the HiFiasm assembly is shown in Figure 1 . The dotplot of contigs >1 Mb in size showed a complete match of 25 contigs (out of total 30) with the 14 Hi‐C pseudo‐molecules (Sharma et al., 2021b ) (Figure 1a ). The remaining five large contigs did not contribute to the genome assembly.…”

“…These contigs alone provided a good assembly with an N50 of 46 Mb and a busco score of 99.1% (Table 1 ). Dotplot analysis against the Hi‐C assembly (Sharma et al., 2021b ) showed that, of the nine contigs more than 46 Mb in length, eight correspond to complete Hi‐C pseudomolecules (i.e. each contig corresponds to a single chromosome; chromosomes 1, 4, 5, 6, 10, 11, 13 and 14) (Figure 2a ).…”

“…In the present study, we have combined the benefit of the highly accurate reads with an improved assembly tool HiFiasm (Cheng et al., 2021 ). HiFi read genome coverage of 28–40×, for plant genomes within the range of 700−1000 Mb size, was sufficient to generate high quality assemblies with Mb contig sizes (Sharma et al., 2021b ). The DNA extracted from M. jansenii may have contained some impurities that reduced the efficiency of the DNA sequencing.…”

“…We have used Macadamia jansenii to compare methods for the sequencing and assembly of plant genomes (Murigneux et al., 2020 ; Sharma et al., 2021a ). This genome has a size (approximately 800 Mb) typical of many plant genomes but with a relatively low heterozygosity (Sharma et al., 2021b ). Assembly of this genome using highly accurate circular consensus sequencing (CCS) reads (HiFi; PacBio) using the HiFiasm assembly tool (Cheng et al., 2021 ) was found to give a more contiguous genome than that obtained with earlier longer continuous long reads (CLR; PacBio) (Sharma et al., 2021a ).…”