Ecological Population Genomics in the Emerging Amanita System

Abstract

The genus Amanita (Agaricomycetes) is an emerging non-model system for ecological population genomics. Amanita is a charismatic genus of beautiful and sometimes deadly poisonous mushrooms. Several Amanitae are invasive species, including the ectomycorrhizal A. phalloides and saprotrophic A. thiersii. Ecological population genomics combines population genomics, the study of differences within and between populations using genomic data, with ecological perspectives on the contexts of populations and natural history of each specimen. In Chapter 1, I develop AmanitaBASE as a resource and foundation for ecological population genomics in the Amanita system. AmanitaBASE consists of hundreds of physical specimens of Amanita, mushrooms and cultures; associated sequences, including 93 whole genomes, 52 of which are from the same two populations over three timepoints: 2004, 2014, and 2015; metadata about specimens including GPS coordinates, dates of collection, exact positions of collected specimens, photos of specimens, and descriptions of the surrounding area; and protocols and best practices developed alongside and as part of AmanitaBASE. The data in AmanitaBASE serves as the basis for Chapter 2 and parts of Chapter 3. In Chapter 2, I survey a natural population of highly variable mating compatibility genes, HD1 and HD2, by sequencing directly from specimens collected from the field. Compatible mates must have different HD1 and HD2 alleles, therefore diversity at HD1 and HD2 has a large effect on the mating dynamics of the population. Yet, because of difficulties with sequencing the region, it has been difficult to study HD1 and HD2 directly from natural populations. Without population-level data, it has been difficult to determine the source of the high multiallelism typically found in HD1 and HD2 across Basidiomycetes. This study pioneers the use of next generation sequencing to study the HD locus in its natural context and methods for obtaining the sequences of HD1 and HD2. Methods for phasing haplotypes are discussed. I conclude that the diversity of HD1 and HD2 alleles is ancient and maintained by balancing selection rather than continuously generated by ongoing negative frequency-dependent selection on new variation. Chapter 3: Contributions to the Amanita system is a collection of smaller projects and work to which I contributed. Section I suggests a new lens for viewing “individuality” in filamentous fungi, in which the mycelium is less the individual in itself and more a shared resource for its constituent nuclei. The degree of conflict or integration in the interests of the nuclei determines how well-integrated of an individual a mycelium. Section II describes a population genetic analysis of the AmanitaBASE data to determine the size of genets in A. phalloides. Section III describes my investigation into the apparent loss of the HD1 mating gene in A. thiersii and its implications for A. thiersii’s rapid invasion of the Eastern US and low genetic diversity across its range. Section IV details the sequencing and assembly of A. phalloides genome Dr4M1 in advance of the massively parallel AmanitaBASE project and the early exploration of MSDIN toxins in the A. phalloides genome. Relevant history of the Amanita system is included throughout. Together, these chapters explore the ecological population genomics of Amanita in breadth and depth, with a focus on discovery science in the development of resources in the Amanita system.