PhD defence: Knud Nor Nielsen (by videolink)

Knud Nor Nielsen defends his thesis,

Population genomics and biology of the fungal pathogen Neonectria neomacrospora

by video link

Associate professor Ole Kim Hansen, IGN
Senior adviser Iben Margrete Thomsen, IGN

Assessment Committee:
Professor Eva Holtgrewe Stukenbrock, Christian Albrechts University of Kiel - Germany
Senior Researcher Mark McMullan, The Earlham Institute, Norwich - UK
Professor Erik Dahl Kjær (chair), IGN

The thesis aims to further our understanding of the diversity, population structure and demographic history of the fungal pathogen Neonectria neomacrospora, in a range-wide context. The thesis consists of an introduction and four papers:
Paper 1: The pangenome of the fungal pathogen Neonectria neomacrospora. This paper is a genome announcement of the first whole-genome sequence of Neonectria neomacrospora. The isolate was collected in Silkeborg Nordskov, Denmark, sequenced using third-generation sequencing (TGS), and the complete nuclear and mitochondrial genome of this isolate was
assembled. In addition to the gapless genome assembly of isolate KNNDK1, the authors present the pangenome of N. neomacrospora, describing the within-species variation in genome content across the species, based on 61 genome assemblies. We identify speciesspecific genomic characteristics of N. neomacrospora by comparison to a suite of genomes
assembled from fifteen other Sordariomycete species. Significant intraspecies genome size differences between populations were revealed. Isolates with the smallest genomes formed a monophyletic group consisting of all strains from Europe and Quebec. We describe the repertoire of carbohydrate-active enzymes, a repertoire consistent with a hemibiotrophic lifestyle.
Paper 2: Population genomics of the emerging forest pathogen Neonectria neomacrospora. Within this study, the authors investigate the hypothesis that the current European epidemic of Neonectria neomacrospora is caused by a recent introduction of a more virulent Quebec lineage of the fungus to Europe. We analyze the population structure, and demographic history of N. neomacrospora inferred from whole-genome shotgun sequencing of 64 strains sampled from China, Europe and North America. We find a substantial gene flow from the North American to the European population, and learnt that the European population shows signs of having lost genetic variation and subsequently expanded in size. The data do not support the hypothesis that the current epidemic of N. neomacrospora is caused by a recent introduction from Quebec.
Paper 3: Direct quantitative real-time PCR assay for detection of the emerging pathogen Neonectria neomacrospora. Effective monitoring of Neonectria neomacrospora calls for a rapid and sensitive method of identification and quantification. This paper describes the development of a probe‐based real‐time PCR (qPCR) assay based on the β‐tubulin gene. This molecular assay is intended for the detection and quantification of N. neomacrospora in infected wood samples, on insects, or within bioaerosol samples.
Paper 4: The effect of temperature on ascospores release within Neonectria neomacrospora. This paper describes a small study on winter hardiness of ascospore dispersal by Neonectria neomacrospora. It is shown that N. neomacrospora can release ascospores in mid-winter at temperatures down to zero degrees Celsius. Clusters of perithecia kept at zero degrees Celsius can continue to release ascospores at a low rate for at least 12 days.

A digital version of the PhD thesis is available with the PhD secretary Anne Marie Faldt,