Program Book - 27th Fungal Genetics Conference

FULL POSTER SESSION ABSTRACTSthe loci on chromosome five in two of the populations. The reduced pair-wise linkage disequilibrium with increasing distance cannot be attributed tomutation alone, and thus the high intrachromosomal recombination is most likely due to meiotic recombination following outcross in these populations.Recombination hot spots and cold spots were detected. Mating type loci in 59 isolates of two populations were genotyped using PCR with allele-specificprimers. About 40% of the isolates showed both MAT1-1 and MAT 1-2 idiomorphs, as expected for a homothallic species. However, the remaining 60% ofthe isolates had only the MAT1-2 idiomorph as detected by the allele-specific PCR. Although the nature of the absence of the MAT1-1 idiomorph remainsto be determined, the results showed variations in mating type alleles in natural populations, suggesting that some of the isolates may not be trulyhomothallic.681. Population genomics of Suillus brevipes. Sara Branco, John Taylor, Tom Bruns. Plant and Microbial Biology, University of California, Berkeley, CA.Environmental heterogeneity may result in divergent selection, which in turn may lead to local adaptation resulting in populations showing habitat-baseddiscontinuous variation. Very little is known on the patterns of adaptive divergence and local adaptation or underlying selective forces in ectomycorrhizalfungal populations. We are studying the population genomics of Suillus brevipes (Peck) Kuntze, an ectomycorrhizal fungus associated with pine trees. Ourgoals are 1) to test the existence of barriers to gene flow across populations, and 2) detect genomic regions exhibiting selection sweeps. We sequencedthe whole genomes of 30 S. brevipes individuals from two populations, one from a coastal Bishop pine forest in Mendocino Co (CA) and another from ahigh altitude Lodgepole pine forest in Yosemite National Park (CA). One isolate was selected as the reference strain and its genome was assembled denovo through a collaboration with the Joint Genome Institute. All other individuals were aligned to this reference and single nucleotide polymorphismsdetected across populations. These markers are being used to find regions with evidence of positive natural selection, including possible islands ofintrogression, increased rates of non-synonymous substitutions, accelerated rates of divergence, and gene duplications. Results from our study will make asignificant contribution for understanding patterns of neutral and functional variation as well as gene flow and selection in ectomycorrhizal fungi.682. Ugly, understudied and undertreated: population genomics of the most common human fungal pathogen - the dermatophyte Trichophytonrubrum. M. Gajdeczka, W. Li, J. Heitman. Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC.Trichophyton rubrum causes athlete’s foot, nail infections and ringworm in about twenty percent of the general population. Despite an annotatedgenome and hundreds of clinical isolates, the global genomic diversity and population biology of T. rubrum are not well understood. Additionally, T.rubrum cannot be crossed, genetic manipulation is difficult, and animal infections with T. rubrum are acute and highly inflammatory (rather than chronicand relatively mild as in humans). These factors have made it difficult to study virulence in T. rubrum and have limited the development of effectivechemotherapies. This study will test three hypotheses: (1) clonal reproduction and limited dispersal have resulted in undiscovered local sequence variationand linkage disequilibrium (LD); (2) observed variation supports an out-of-Africa isolation-by-distance migration model; and (3) patterns of sequencediversity in sex- and virulence-associated genomic regions support the significant evolutionary roles of reproductive clonality and close interaction withhumans. Worldwide isolates appear reproductively clonal and remarkably genetically monomorphic. Five common MLST markers reveal no variationamong 50 European, Asian and North American strains. We Sanger sequenced 7.5 kb of non-coding intergenic regions in ten T. rubrum isolates collectedover a span of ten years. These sequences revealed no polymorphisms useful for differentiating strains. Lastly, VNTR genotyping by our lab and othergroups revealed two broad geographic types, though these are based on a few highly variable loci subject to homoplasy. We are assembling wholegenome sequences of 32 geographically and clinically diverse strains to characterize sequence diversity more completely. The genome obtained by theBroad Institute will be used as a reference. We will obtain measures of diversity, polymorphism, LD, population differentiation and divergence. Thesemeasures will be used to compare isolates genome-wide, determine population structure and infer evolutionary and demographic forces contributing toobserved patterns of variation. Locus-specific markers will be developed based on standing variation to genotype additional strains. Furthermore, we willtest for variants associated with hypothesized virulence mechanisms involved in chronic T. rubrum infection.683. Poppr: an R package for genetic analysis of populations with mixed reproduction. Zhian N. Kamvar 1 , Niklaus J. Grünwald 1,2 . 1) Botany and PlantPathology, Oregon State University, Corvallis, OR; 2) USDA-ARS Horticultural Research Laboratory, Corvallis, OR.Analysis of populations with mixed reproductive systems, including a blend of sexual and clonal reproduction, remains a challenge. We developed an Rpackage implementing existing approaches for analysis of mixed populations. R is a multi-platform, open source, statistical environment that has gainedpopularity over the past few years. While there are a plethora of packages in R that perform population genetics analyses, many standard analysismethods for populations with mixed modes of reproduction remain hard to accomplish. Poppr aims at providing functions to facilitate rapid analyses ofthis data, particularly including methods for analysis of recombination (index of association), clone-censored analysis of full datasets in a hierarchicalmanner over all levels of sampling, genotypic diversity analyses, and distance analyses. As implemented, poppr requires minimal commands withconvenient summary functions while providing compelling graphics. Unlike many platform dependent, standalone programs, poppr can be used for batchprocessing of data including all kinds of population genetic data (dominant/codominant; microsatellites, AFLP, SNPs). Poppr is available as a beta releasefor testing upon request and continues to be improved.684. The heterothallic fungus Cercospora beticola contains fragments of both mating type genes. Melvin D. Bolton 1 , Zhaohui Liu 2 . 1) USDA - ARS, Fargo,ND; 2) North Dakota State University, Department of Plant Pathology, Fargo, ND.In most heterothallic Ascomycota, the ability to reproduce sexually is determined by a single mating type locus (MAT1) represented by two idiomorphsknown as MAT1-1 and MAT1-2 that are required to control nonself-recognition and mating of compatible partners. To investigate the MAT1 locus in theheterothallic fungus Cercospora beticola, we performed Southern analyses of both mating types using each mating type gene (MAT1-1-1 and MAT1-2-1) asa probe. Surprisingly, several bands of similar size were observed in both mating types using either probe, suggesting that multiple loci contain sequencesof both MAT genes in the C. beticola genome. We screened a BAC library derived from a MAT1-2 isolate using both MAT gene probes to identify clonescontaining MAT gene sequences. Sequence analysis of four BAC clones confirmed that one BAC contained the true MAT1-2 idiomorph, while the otherthree contained fragments of both MAT genes in close proximity (8 to 1,075 bp) to each other. To investigate whether this holds true in the oppositemating type, we sequenced the identical regions in a MAT1-1 isolate. Sequence analysis confirmed that the MAT1-1 isolate contained one full MAT1-1idiomorph as well as additional regions that contained fragments of both MAT genes. In all cases, introns normally present in MAT genes were not presentin the MAT1-1-1 or MAT1-2-1 gene fragments in either mating type. Although heterothallism has been suggested to be the ancestral state in theDothideomycetes, the identification of fragments of both mating types in a single isolate suggests that homothallism is the ancestral state in C. beticola.685. Population structure from mountain to coast of two Lophodermium endophytes; a case study comparing rare and common fungal species in pineneedles. Ryoko Oono 1,2 , Laurel Koch 1 , A. Betsy Arnold 3 , Georgiana May 4 , François Lutzoni 1 , Ignazio Carbone 2 . 1) Department of Biology, Duke University,27th Fungal Genetics Conference | 289