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156625251.Pdf View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by The Australian National University Mycologia, 107(1), 2015, pp. 217–226. DOI: 10.3852/13-278 # 2015 by The Mycological Society of America, Lawrence, KS 66044-8897 Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology Andrew W. Wilson1 methods to identify cryptic species. F-statistics were Chicago Botanic Garden, Plant Conservation Science, easily calculated, although an observable ‘‘noise’’ was 1000 Lake Cook Road, Glencoe, Illinois 60022 detected when using the ‘‘All Loci’’ treatment versus Norman J. Wickett filtering loci to those present in at least 50% of the Chicago Botanic Garden, Plant Conservation Science, individuals. The data were analyzed with tests of 1000 Lake Cook Road, Glencoe, Illinois 60022; Hardy-Weinburg equilibrium, population genetic Northwestern University, Program in Biological statistics (FIS and FST), and population structure Sciences, 2205 Tech Drive O.T. Hogan Hall Room analysis using the program Structure. The results 2-144, Evanston, Illinois 60208 provide encouraging feedback regarding the poten- Paul Grabowski tial utility of these methods and their data for University of Chicago, Ecology and Evolution, 1101 E population genetic analysis. We were unable to draw 57th Street, Chicago, Illinois 60637 conclusions of life history of L. bicolor populations Jeremie Fant from this dataset, given the small sample size. The Chicago Botanic Garden, Plant Conservation Science, results of this study indicate the potential of these 1000 Lake Cook Road, Glencoe, Illinois 60022 methods to address population genetics and general life history questions in the Agaricales. Further Justin Borevitz research is necessary to explore the specific applica- Australian National University, Research School of Biology, Canberra, Australia; University of Chicago, tion of these methods in the Agaricales or other Ecology and Evolution, 1101 E 57th Street, Chicago, fungal groups. Illinois 60637 Key words: Agaricales, Agaricomycetes, Fungi, Gregory M. Mueller GBS, RAD, restriction-site associate DNA Chicago Botanic Garden, Plant Conservation Science, 1000 Lake Cook Road, Glencoe, Illinois 60022 INTRODUCTION Fungi are involved in a vast array of ecological Abstract: Given the diversity and ecological impor- interactions. They are also one of the most cryptic tance of Fungi, there is a lack of population genetic groups of multicellular eukaryotic organisms. Deter- research on these organisms. The reason for this can mining the size and number of individuals in a be explained in part by their cryptic nature and population and the genetic relationships among difficulty in identifying genets. In addition the populations is needed for understanding microevolu- difficulty (relative to plants and animals) in develop- tionary and ecological processes. Studying fungal ing molecular markers for fungal population genetics populations is best accomplished with molecular contributes to the lack of research in this area. This methods because of challenges identifying individuals study examines the ability of restriction-site associated (genets) based on sporocarp demographic patterns. DNA (RAD) sequencing to generate SNPs in Laccaria However, relative to plants and animals, population bicolor. Eighteen samples of morphologically identi- genetic studies in fungi are lacking. Only 8% of the fied L. bicolor from the United States and Europe population genetic studies appearing in Molecular were selected for this project. The RAD sequencing ecology 2009–2010 involved fungi (Guichoux et al. method produced anywhere from 290 000 to more 2011) and less than 7% of the population genetics than 3 000 000 reads. Mapping these reads to the papers published in Molecular Ecology Notes 2001– genome of L. bicolor resulted in 84 000–940 000 2005 focused on fungi (Dutech et al. 2007). Further- unique reads from individual samples. Results indi- more, a review of landscape genetic studies stated that cate that incorporation of non-L. bicolor taxa into the only 0.5% of these studies involved fungi (Storfer et analysis resulted in a precipitous drop in shared loci al. 2010). A review of population genetics of among samples, suggests the potential of these ectomycorrhizal fungi demonstrated that the accu- mulation of studies in this field has grown linearly Submitted 31 Aug 2013; accepted for publication 4 Oct 2014. 1990–2009 (Douhan et al. 2011), but fungal popula- 1 Corresponding author. E-mail: [email protected] tion studies still are relatively rare. By basis of 217 218 MYCOLOGIA comparison, the proportion of fungal population animals (Guichoux et al. 2011, DeFaveri et al. 2013) genetic studies 1990–2009 made up only 1–2% of but have yet to be used for population studies of population genetic studies as a whole (evaluation Agaricales. SNPs are easily identified, are co-domi- using ISI Web of Science and the search terms ‘‘fungi nant and occur in such high numbers that in some population genetics’’ and ‘‘population genetics’’). cases they can be more efficient than SSRs because The paucity of research in fungal population they do not require large sample sizes to characterize genetics has left mycologists with many unanswered variation within a population nor do they need questions as to how ecological roles, life histories and common controls across studies and time (Guichoux evolutionary relationships shape fungal populations. et al. 2011). However, as with SSRs, accumulating Considering there are more than 1 500 000 estimated sufficient SNP data in fungi has been problematic due species of fungi and all of the ways these fungi to laborious Sanger sequencing of limited loci (Keirle contribute to the environment—from ecosystem et al. 2011). services, to associations with foundation species—the Restriction-site associated DNA (RAD) sequencing underrepresentation of population genetic studies in is a relatively new method using high-throughput fungi needs to be addressed. Several factors might sequencing technology that allows for identification contribute to the dearth of fungal population genetic of SNPs by sequencing many small fragments in research including complications of collecting suffi- highly variable regions of the genome accessed cient samples of these cryptic organisms and chal- through restriction digest (Miller et al. 2007). The lenge of developing population genetic markers for more closely related a group of organisms are, the studying fungi. more restriction loci they will have in common A small number of studies have attempted to throughout their genome. Because of this principal, characterize the population genetic structure of some RAD sequencing has been demonstrated as an Agaricales (mushroom-forming fungi). Studies of the effective way to generate homologous loci from which ECM fungus Russula brevipes identified distinct popu- SNPs can be identified for population genetic lations only over very long distances (. 1500 km) analysis. Elshire et al. (2011) developed a simplified (Bergemann and Miller 2002) but was unable to detect RAD sequencing approach for genotyping by se- population structure at shorter distances (, 1 km) quencing (GBS). This method recovered . 25 000 (Bergemann et al. 2006), both studies relied on only and 436 biallelic SNP markers from maize and barley, three and six SSR (short sequence repeats, AKA respectively. The ability of these techniques to identify microsatellites), respectively. A study of European a large number of SNP loci in a genome has the Laccaria amethystina populations using a combination potential to overcome the limitations of traditional of SSRs, a mitochondrial marker, and direct amplifi- marker development in fungal population genetics cation of length polymorphism (DALP) was not able to (Davey and Blaxter 2011, Davey et al. 2011, Elshire et detect reproductive isolation among populations al. 2011, Morris et al. 2011, DeFaveri et al. 2013). separated by distances . 400 km (Roy et al. 2008). This study tests the effectiveness of RAD sequenc- Similarly Keirle et al. (2011) showed that Hawaiian ing by with the GBS approach developed by Morris et populations of the saprobe fungus Rhodocollybia al. (2011) to detect SNP markers in a small sampling laulaha were not shaped by the geological history of of the ectomycorrhizal mushroom species Laccaria the Hawaiian Islands, although this analysis was limited bicolor. This study also examines the efficacy of this to a single genetic marker. The restricted number of method given taxonomic ambiguities related to the markers used in these studies limited the resolution test species. Last, this study uses the availability of the and potential for a clear assessment of gene flow or L. bicolor genome to test whether a reference genome understanding evolutionary history within these is necessary for analyzing population genetic structure groups. with SNPs in Agaricales. Although SSRs are commonplace in population genetic studies of plants and animals, their usefulness MATERIALS AND METHODS in studying fungal populations appears to be limited. Dutech et al. (2007) enriched the SSR libraries for 17 Sample selection and phylogenetic evaluation of samples.— species of fungi and concluded that SSRs are not only Eighteen samples, consisting of Laccaria species morpho- logically identified as L. bicolor (n 5 7) and L. trichodermo-
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