Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9 –12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.

We used long read sequencing data generated from Knightia excelsaI R.Br, a nectar producing Proteaceae tree endemic to Aotearoa New Zealand, to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome construction. Establishing a high-quality genome for this species has specific cultural importance to Māori, the indigenous people, as well as commercial importance to honey producers in Aotearoa New Zealand. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies, and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Assemblies that used longer read lengths (>30 kb) and lower coverage were the most contiguous, kmer and gene complete. The final genome assembly was constructed into pseudo-chromosomes using all available data assembled with FLYE, polished using Racon/Medaka/Pilon combined, scaffolded using SALSA2 and AllHiC, curated using Juicebox, and validated by synteny with Macadamia. We highlighted the importance of developing assembly workflows based on the volume and type of sequencing data and establishing a set of robust quality metrics for generating high quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by utilizing Hi-C data and that scaffolded assemblies were more accurate when the underlying contig assembly was of higher accuracy. These findings provide insight into what is required for future high-quality de-novo assemblies of non-model organisms.