| Summary: | New Zealand has an interesting history that has shaped its biota through its isolation, almost total absence of terrestrial mammals and climate history. This history is thought to have influenced, for instance, the evolution of flightless birds, rapid speciation and morphological diversification of vascular alpine plants, the high abundance of brightly coloured, epigeous sequestrate fungi and the disjunct distribution of the mycorrhizal host species Nothofagus . However, inferences concerning such concepts are reliant on accurate and informative data, in particular a complete and robust taxonomic treatment of species involved, supported by appropriate genetic data. This thesis concerns three different areas. Firstly, the systematics of selected species from the New Zealand mycorrhizal genus, Cortinarius . Secondly, automated data retrieval of BLAST search results and associated sequences from the same vouchered specimen. Finally, the potential utility of chloroplast genomes in population genetics of a one of the most wide spread mycorrhizal fungal host species, Nothofagus menziesii . Accurate taxonomy is fundamental for communicating species concepts and critical in many biological disciplines including biodiversity analyses, conservation and life history studies. Fungi are the second most diverse group of eukaryotic organisms on the planet after insects. Twelve million species are thought to be in the fungal kingdom, with only ca. 120 000 currently described. Cortinarius is a widely distributed genus of ectomycorrhizal fungi in the Agaricales, present in temperate and subarctic-alpine climates in both hemispheres. Cortinarius is highly diverse; with over 3000 species described it is the largest genus in the Agaricales. In New Zealand, Cortinarius is the dominant ectomycorrhizal genus and associates with Nothofagus , Kunzea and Leptospermum . Members of the genus display a wide range of colours from white to almost black, and almost every colour in between. The sexual fruit bodies of Cortinarius taxa are mostly agaricoid in morphology, but many species have a gasteroid or secotioid morphology. In this thesis, new species of sequestrate and agaricoid Cortinarius are described, covered in chapters 2–4. In particular, four additional species of purple secotioid species were discovered to be hidden under the name of the iconic C. porphyroideus . Members of Cortinarius section Subcastanelli were also investigated. It was discovered that the protologue of C. subcastanellus was based on multiple taxa, other members of this section were found to be synonyms of earlier species. In total seven new Cortinarius species were described, three synonymisations and one emendation are made. The second objective was to ameliorate some of the manual data retrieval and cleaning for multigene phylogenetics, particularly in relation to fungal taxonomy. In chapter 5, the python script multigene_blastnparse.py is presented. This script retrieves BLAST matches from Genbank and all other markers from the same specimen identifier. BLAST matches are written to a csv file for immediate overview, while the sequences are written to a file in fasta format. All headers in the primary field of the fasta file are unique for each specimen identifier allowing for seamless concatenation of sequences from different regions for multigene phylogenetics. This bioinformatics tool is used in a subsequent chapter and is freely available on GitHub. Nothofagus is a dominant and widely distributed tree genus in New Zealand. It is one of three genera that host ectomycorrhizal fungi, upon which they are dependent for much of their mineral nutrient acquisition. Nothofagus in New Zealand displays an interesting disjunct distribution on the South Island of New Zealand where it is missing in central Westland, known as the Westland beech gap. Many hypotheses and studies have been put forward for the presence and persistence of the Westland beech gap, including the lack of mycorrhizal symbionts in the beech gap preventing the expansion of Nothofagus into the area. However, there is a paucity of genetic data for confident conclusions to be drawn. Chloroplast markers are often used in population genetic studies as they are generally unilaterally inherited and geneflow is restricted to seed dispersal. However, most traditional chloroplast markers are slow evolving genes that are not suited to population genetics. Advances in sequencing has enabled high throughput sequencing of whole chloroplast genomes. Whole chloroplast genomes have been found to contain highly variable regions between populations, making them valuable for population genetics. Either through identification of variable regions for studies using traditions techniques, or used in their entirety. In chapter 6, the chloroplast genome of Nothofagus menziesii from a Dunedin individual was sequenced and assembled using short and long read sequencing technologies. The chloroplast genome was 156 145 kb and presented a typical quadripartite structure. The genome contained 130 genes and was comparable to other chloroplast genomes in the Fagales. A chloroplast genome was sequenced using genome skimming from a geographically distant individual (St Arnaud, ~500 km separation) and compared to the Dunedin individual. The comparison revealed 131 polymorphic sites, with 13 regions less than 700 bp containing more than 3 SNPs. These regions may be valuable for future population genetic studies of Nothofagus menziesii . This thesis makes a significant contribution to the systematics of the mycorrhizal genus Cortinarius in New Zealand. It also accelerates sequence data acquisition for multigene phylogenies. Finally, this thesis presents the first whole chloroplast genomic resource for one of the dominant mycorrhizal fungi host species, Nothofagus menziesii .
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