Source: UNIVERSITY OF CALIFORNIA, BERKELEY submitted to
FUNGAL EVOLUTION: PATHOGEN POPULATION GENETICS/GENOMICS AND IDENTIFICATION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0218570
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2009
Project End Date
Sep 30, 2014
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF CALIFORNIA, BERKELEY
(N/A)
BERKELEY,CA 94720
Performing Department
Microbial Biology
Non Technical Summary
We developed molecular methods to recognize fungal species by genetic isolation in naure and continue to apply this approach to model and socially important fungi. We discovered mate choice in microbes and aim to find the genes that allow female fungi to reject suitors from other species. We have conducted the first comparative genomic study of a human pathogenic fungus and now aim to extend our efforts to account for population variation. To associate phenotypic and genetic variation, we have used quantitative trail locus mapping and now are moving to whole genome association mapping, following the lead of human geneticists. We have profiled RNA transcription in Coccidioides using microarrays of 1000 genes and now are moving to profiling all genes by sequencing the RNAs. We aim to automate identification of fungi to support ecological and agricultural research.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2124020108010%
2124020110230%
3114020108010%
3114020110210%
3114020117010%
7024020110210%
7124020108010%
7124020117010%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 311 - Animal Diseases; 702 - Requirements and Function of Nutrients and Other Food Components; 712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins;

Subject Of Investigation
4020 - Fungi;

Field Of Science
1102 - Mycology; 1080 - Genetics; 1170 - Epidemiology;
Goals / Objectives
We are studying fungal species in terms of their genetic isolation and adaptation.We now focus on one animal pathogenic genus, Coccidioides, and one plant-associated genus, Neurospora.Additionally, we apply our knowledge to fungi of social importance as the need arises,e.g. in the past period, we also investigated the amphibian pathogen, Batrachochytrium and the animal pathogen, Paracoccidioides, and the plant-associated fungus, Aspergillus fumigatus.1.First objective is phylogenetic species recognition and estimation of reproductive mode as clonal or recombining.The goal is to determine the limits of species based on genetic isolation in nature as measured by concordance of gene genealogies. Expected outcome is a phylogeny and results of tests for recombination or clonality.2.Second objective is to compare fungal genomes within and among closely related species to identify genes important to adaptation.The goal is to discover gene family expansion/contraction, gene gain/loss, rapid gene evolution, and selection.The outcome will be a list of genes prioritized for gene disruption studies to determine if these genes are important to adaptation.3.Third objective is to discover the genes important to species maintenance in sympatry by reinforced reproductive isolation.The goal is to identify genes that have evolved for reinforcement.We now are using transcription profiling in crosses that result in mature perithecia and aborted perithecia to identify genes in our known QTL that are important to reinforcement.The outcome will be genes whose disruption affects reproduction.4.Fourth objective is to develop a community tool to rapidly associate phenotype and genotype in Neurospora.This project builds on our success with QTL analysis in objective3.Here, we are using both QTL and an approach developed for human genomics, Whole Genome Association (WGA). With QTL, the phenotypes are limited to those that vary in the parents or in the progeny, mapping population and the association is limited by the length of genetic blocks in linkage disequilibrium.WGA avoids these limitations because the population involves hundreds of wild isolates with more phenotypic trait variation than any pair isolates, and because the wild, outbred population has relatively shorter recombination blocs.The goal is to associate complex phenotypes with specific genes or other genome regions.The outcome is a collection of genes hypothesized to be important to the trait of interest. Yet again, disruption of these genes and assessment of the relevant phenotypes will tell if the approach has succeeded.5.Fifth objective is to develop a work-flow to identify the fungi in environmental samples based on DNA.The goal is to identify fungi in environmental samples by extracting DNA from the sample, PCR amplifying a genome region that is diagnostic for fungal species (ITS of rDNA), sequencing the amplified regions, identifying the sequenced regions by phylogenetic comparison of the new, unknown sequences with known sequences.The outcome is a list of species and their abundance in an environmental sample. Output activities center on teaching and mentoring, conferences, workshops and symposia.
Project Methods
1. To recognize phylogenetic species, we use concordance of multiple gene genealogies. This approach relies on sequence data of four to five genes that are polymorphic in a morphological species. Where gene genealogies move from congruence to conflict, species are identified. 2. For QTL, we mate parents with different character states for the phenotypic trait and with genetic variation. We then score 500 progeny for the trait and for genetic variation. Association of the trait and genetic markers places the QTL on the marker map. 3. For genome comparison, we assemble, annotate and align the genomes and then use tools appropriate for analysis at different levels of phylogenetic divergence. Gene family size change is studied with deep divergences and large numbers of genomes, gene gain and loss is studied at shallower divergences with just four taxa. Rates of evolution is studied at even shallower divergences with just three taxa, and selection is studied among very close relatives, i. e., sister species, with just two species. 4. Our WGA project focuses on 200 individuals from the Caribbean population of Neurospora crassa and we are assessing both transcription and characterizing single nucleotide polymorphisms through next generation sequencing of mRNAs. 5. To profile transcription in Coccidioides species we are using next-generation sequencing of mRNAs (RNA-seq). 6. To characterize fungi in environmental samples, we extract DNA, amplify the rDNA ITS region, and sequence it. Sequences are identified by phylogenetic analysis with known ITS sequences.

Progress 10/01/09 to 09/30/14

Outputs
Target Audience: Our research is aimed at scientists in industry or academia who could benefit from using natural variation to aid studies of molecular development, who could benefit from using new methods of assessing fungi in indoor air, or who could benefit from knowing genes important to natural adaptation in human pathogenic fungi. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Graduate students. Two are currently being trained, C. Hann-Soden and I. Sylvain. Postdocs. One postdoc won a permanent research position in France, Dr. Pierre Gladieux, INRA in Montpellier, Fr. One postdoc won a research position in industry, Dr. Emily Whiston aty Envirogix in Portland, Me. Three postdocs continue in the lab, Dr. Rachel Adams, Dr. Sara Branco and Dr. Marie Donnelly. How have the results been disseminated to communities of interest? Our research was published in six, peer-reviewed articles in 2014. Talbot, J.M., Bruns, T.D., Taylor, J.W., Smith, D.P., Branco, S., Glassman, S.I., Erlandson, S., Vilgalys, R., Liao, H.-L., Smith, M.E., Peay, K.G. 2014. Edemism and functional convergence across the North American soil mycobiome. PNAS (doi: 10.1073/pnas.1402584111). PMID: 25557275 Corcoran, P., Dettman, J. R., Sun, Y., Luque, E. M., Corrochano, L. M., Taylor, J. W., Lascoux, M., Johannesson, H., 2014. A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system. Molecular Phylogenetics and Evolution. 78, 136-147. PMID: 24845789 Liao, H. L., Chen, Y., Bruns, T. D., Peay, K. G., Taylor, J. W., Branco, S., Talbot, J. M., Vilgalys, R., 2014. Metatranscriptomic analysis of ectomycorrhizal roots reveal genes associated with Piloderma-Pinus symbiosis: Improved methodologies for assessing gene expression in situ. Environmental Microbiology. n/a-n/a. DOI:10.1111/1462-2920.12619 PMID: 25186788 Pitt, J. I., Taylor, J. W., 2014. Aspergillus, its sexual states, and the new International Code of Nomenclature. Mycologia 106:1051-1062, doi:10.3852/14-060. PMID: 24871603 Ellison, C.E., Kowbel, D, Glass, N.L., Taylor, J., Brem, R.B. 2014. Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates. mBio 5(2) 2e01046-13. doi: 10.1128 /mBio.01046-131. PMID: 24692637 Adams, R. I., Miletto, M., Lindow, S. E., Taylor, J. W., Bruns, T. D., 2013b. Airborne bacterial communities in residences: Similarities and differences with fungi. Plos One. 9: e91283. PMID: 24603548 Adams, R. I., Miletto, M., Taylor, J. W., Bruns, T. D., 2013b. The Diversity and Distribution of Fungi on Residential Surfaces. Plos One. 8. PMID: 24223861 What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We use nucleic acid variation as a tool to 1) identify fungi, 2) recognize fungal species and populations, 3) identify gene flow among populations, 4) find genes important to adaptation, 5) assign function to unknown genes, 6) characterize fungal communities in soil, air, food and animals and 7) characterize fungal activity in nature through their transcripts and proteins. We disseminate our results by publications and presentation at scientific meetings, both posters and oral presentations. Our immediate goals are listed below: 1. We aim to characterize the ability of fungi isolated from decaying biofuel plants to deconstruct plant cell walls with the goal of improving enzymes used to convert plant biomass to transportation fuels. 2. We aim to use genome wide association to find genes behind traits of thermophilic yeasts important to their use in producing biofuels. 3. We aim to use next-generation-sequencing of mRNA from Neurospora discreta to investigate the role of fungi in global climate change in the Boreal Forest. 4. We aim to use population genomics with two populations of ectomycorrhizal fungi to study their adaptation to coastal and montane forests. 5. We aim to use population genomics of Neurospora discreta collected throughout western North America to study gene flow and adaptation in this fungus, which is capable of bioconversion of plant biomass. What was accomplished under these goals? 1. Our manuscript reporting on our characterization of fungi isolated from decaying biofuel plants has been accepted for publication and will be reported in our 2015 AES report. Ours is the most complete such study using 30 fungi and characterizing biomass conversion, enzyme activity and removal of specific fungal cell wall components. 2. We have sequenced more than 30 thermophilic yeasts and have characterized biofuel phenotypes for the same fungi. We now are analyzing the data to search for genes involved in the traits. 3. We have obtained mRNA from N. discrete individuals acclimated, adapted and evolved to life at higher temperatures and are preparing libraries for RNAseq. We are preparing a ms on the adaptation of N. discrete to life at higher temperatures for submission in 2015. 4. We have sequenced more than 35 strains of Suillus brevipes from coastal and montane California. Comparison of these genomes has discovered a gene involved in salt transport that has evidence of sweeping through the coastal population. This research is in review and will be published in 2015. 5. We have sequenced more than 40 strains of Neurospora discreta and have found a number of stress-related genes that show evidence of rapid evolution and the first evidence for a natural, hybrid individual, consistent with the hypothesis of abundant hybridization and introgression in wild fungal populations. This research is in a ms being prepared for publication. 6. Our work from previous years has resulted in six publications this year Talbot, J.M., Bruns, T.D., Taylor, J.W., Smith, D.P., Branco, S., Glassman, S.I., Erlandson, S., Vilgalys, R., Liao, H.-L., Smith, M.E., Peay, K.G. 2014. Edemism and functional convergence across the North American soil mycobiome. PNAS (doi: 10.1073/pnas.1402584111). PMID: 25557275 Corcoran, P., Dettman, J. R., Sun, Y., Luque, E. M., Corrochano, L. M., Taylor, J. W., Lascoux, M., Johannesson, H., 2014. A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system. Molecular Phylogenetics and Evolution. 78, 136-147. PMID: 24845789 Liao, H. L., Chen, Y., Bruns, T. D., Peay, K. G., Taylor, J. W., Branco, S., Talbot, J. M., Vilgalys, R., 2014. Metatranscriptomic analysis of ectomycorrhizal roots reveal genes associated with Piloderma-Pinus symbiosis: Improved methodologies for assessing gene expression in situ. Environmental Microbiology. n/a-n/a. DOI:10.1111/1462-2920.12619 PMID: 25186788 Pitt, J. I., Taylor, J. W., 2014. Aspergillus, its sexual states, and the new International Code of Nomenclature. Mycologia 106:1051-1062, doi:10.3852/14-060. PMID: 24871603 Ellison, C.E., Kowbel, D, Glass, N.L., Taylor, J., Brem, R.B. 2014. Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates. mBio 5(2) 2e01046-13. doi: 10.1128 /mBio.01046-131. PMID: 24692637 Adams, R. I., Miletto, M., Lindow, S. E., Taylor, J. W., Bruns, T. D., 2013b. Airborne bacterial communities in residences: Similarities and differences with fungi. Plos One. 9: e91283. PMID: 24603548 Adams, R. I., Miletto, M., Taylor, J. W., Bruns, T. D., 2013b. The Diversity and Distribution of Fungi on Residential Surfaces. Plos One. 8. PMID: 24223861

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Talbot, J.M., Bruns, T.D., Taylor, J.W., Smith, D.P., Branco, S., Glassman, S.I., Erlandson, S., Vilgalys, R., Liao, H.-L., Smith, M.E., Peay, K.G. 2014. Edemism and functional convergence across the North American soil mycobiome. PNAS (doi: 10.1073/pnas.1402584111). PMID: 25557275
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Corcoran, P., Dettman, J. R., Sun, Y., Luque, E. M., Corrochano, L. M., Taylor, J. W., Lascoux, M., Johannesson, H., 2014. A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system. Molecular Phylogenetics and Evolution. 78, 136-147. PMID: 24845789
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Liao, H. L., Chen, Y., Bruns, T. D., Peay, K. G., Taylor, J. W., Branco, S., Talbot, J. M., Vilgalys, R., 2014. Metatranscriptomic analysis of ectomycorrhizal roots reveal genes associated with Piloderma-Pinus symbiosis: Improved methodologies for assessing gene expression in situ. Environmental Microbiology. n/a-n/a. DOI: 10.1111/1462-2920.12619 PMID: 25186788
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Pitt, J. I., Taylor, J. W., 2014. Aspergillus, its sexual states, and the new International Code of Nomenclature. Mycologia 106:1051-1062, doi:10.3852/14-060. PMID: 24871603
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ellison, C.E., Kowbel, D, Glass, N.L., Taylor, J., Brem, R.B. 2014. Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates. mBio 5(2) 2e01046-13. doi: 10.1128 /mBio.01046-131. PMID: 24692637
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Adams, R. I., Miletto, M., Lindow, S. E., Taylor, J. W., Bruns, T. D., 2013. Airborne bacterial communities in residences: Similarities and differences with fungi. Plos One. 9: e91283. PMID: 24603548
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Adams, R. I., Miletto, M., Taylor, J. W., Bruns, T. D., 2013. The Diversity and Distribution of Fungi on Residential Surfaces. Plos One. 8. PMID: 24223861


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: Our research is aimed at scientists in industry or academia who could benefit from using natural variation to aid studies of molecular development, who could benefit from using new methods of assessing fungi in indoor air, or who could benefit from knowing genes important to natural adaptation in human pathogenic fungi. Changes/Problems: We change our approach as thinking, tools and instrumentation evolves. An example from 2013 is our switch from 454 to Illumina for sequencing of PCR amplified rDNA for fungal identification. However, our goals remain unchanged from 2013 to 2014. What opportunities for training and professional development has the project provided? Graduate students. One graduate student earner her PhD in 2013, Emily Whiston. Two are currently being trained, C. Hann-Soden and I. Sylvain. Postdocs. Four postdocs were being trained in 2013, Pierre Gladieux, Rachel Adams, Sara Branco and Emily Whiston. How have the results been disseminated to communities of interest? Our reserach was published in five, peer-reviewed articles in 2013 191 Hibbett, D. S. and J. W. Taylor. 2013. Fungal systematics: is a new age of enlightenment at hand? Nature Reviews Microbiology 11: 129-133. 190 Palma-Guerero, J., Hall, C.Rl, Kowbel, D., Welch, J., Taylor, J.W., Brem, R.B., Glass, N.L. 2013. Genome wide association identifies novel loci involved in fungal communication. PLoS Genetics 9: e1003669. 189 Adams, R.I., Amend, A.S., Taylor, J.W., Bruns, T.D. 2013. A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: A case study of fungi in indoor dust. Microbial. Ecol. DOI 10.1007/s00248-013-0266-4. 188 Adams RI, Miletto M, Taylor JW, Bruns TD. 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 21February2013; doi: 10.1038/ismej.2013.28 187 Wise, H-Z, Hung, C-Y, Whiston, E, Taylor, JW, Cole GT. 2013. Extracellular ammonia at sites of pulmonary infection with Coccidioides posadasii contributes to severity of the respiratory disease. Microbial Pathogenesis 59-60: 19-28. What do you plan to do during the next reporting period to accomplish the goals? We have on going projects that address each of our five goals. Isolation and characterization of fungi that naturally decompose energy grasses in nature. Population genomics of Neurospora discreta in nature. Population genomics of ectomycorrhizal fungi in North American forests. Fungal communities in indoor air. Genome wide association in populations of yeast with potential for biofuel production.

Impacts
What was accomplished under these goals? Our accomplishments for each of the five goals listed above: 1. We published a review in Nature Reviews Microbiology about fungal species in the age of genomics; Hibbett, D. S. and J. W. Taylor. 2013. Fungal systematics: is a new age of enlightenment at hand? Nature Reviews Microbiology 11: 129-133. We have used our data on phylogenomics in support of physiological studies of pathogenic fungi. Wise, H-Z, Hung, C-Y, Whiston, E, Taylor, JW, Cole GT. 2013. Extracellular ammonia at sites of pulmonary infection with Coccidioides posadasii contributes to severity of the respiratory disease. Microbial Pathogenesis 59-60: 19-28. 2. and 3. We have the data for a publication on population genomics of Neurospora discreta in western North America, Alaska and Europe that addresses the genetic differentiation and isolation among populations and identifies genes important to adaptation. We expect these data to be published in 2014. 4. We have developed GWAs for fungi and used a small wild population to find 9 genes important to a complex morphological and physiological phenotype, germling signalling and fusion. Palma-Guerero, J., Hall, C.Rl, Kowbel, D., Welch, J., Taylor, J.W., Brem, R.B., Glass, N.L. 2013. Genome wide association identifies novel loci involved in fungal communication. PLoS Genetics 9: e1003669. 5. We have developed a work flow to identify fungi in the environment using next-generation-sequencing and are using it to study fungi in the built evironment, that is, indoor air. Adams, R.I., Amend, A.S., Taylor, J.W., Bruns, T.D. 2013. A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: A case study of fungi in indoor dust. Microbial. Ecol. DOI 10.1007/s00248-013-0266-4. Adams RI, Miletto M, Taylor JW, Bruns TD. 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 21February2013; doi: 10.1038/ismej.2013.28

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Hibbett, D. S. and J. W. Taylor. 2013. Fungal systematics: is a new age of enlightenment at hand? Nature Reviews Microbiology 11: 129-133.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Palma-Guerero, J., Hall, C.Rl, Kowbel, D., Welch, J., Taylor, J.W., Brem, R.B., Glass, N.L. 2013. Genome wide association identifies novel loci involved in fungal communication. PLoS Genetics 9: e1003669.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Adams, R.I., Amend, A.S., Taylor, J.W., Bruns, T.D. 2013. A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: A case study of fungi in indoor dust. Microbial. Ecol. DOI 10.1007/s00248-013-0266-4.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Adams RI, Miletto M, Taylor JW, Bruns TD. 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 21 February 2013; doi: 10.1038/ismej.2013.28
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wise, H-Z, Hung, C-Y, Whiston, E, Taylor, JW, Cole GT. 2013. Extracellular ammonia at sites of pulmonary infection with Coccidioides posadasii contributes to severity of the respiratory disease. Microbial Pathogenesis 59-60: 19-28.


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: Activities. We published work in our two main areas this year, studies of the animal pathogenic fungus Coccidioides immitis and Coccidioides posadasii, and studies of natural populations of the wild fungus, Neurospora. With the animal pathogens we used transcription profiling by next-generation sequencing to investigate gene expression in the saprobic and pathogenic phases (Whiston et al. 2012). The most notable finding is that an uncharacterized gene, 509, is strongly upregulated in the pathogenic phase. This gene is at the left edge of a region introgressed from the Arizona population of C. posadasii into the Southern California population of C. immitis, a position consistent with natural selection for the gene and a role in adaptation. We are currently collaborating with Prof. G. Cole at the University of Texas, San Antonio, in experiments to test this hypothesis. Our work on Neurospora has now extended to a population of N. tetrasperma at the limit of its distribution in the British Isles (Corcoran et al. 2012). The most interesting aspect of this research is that this population of the pseudohomothallic fungus, N. tetrasperma, is acting like a heterothallic fungus in that it produces far more haploid, homokaryotic ascospores than do other populations. This observation is consistent with a fungus whose distant ancestors were outbreeding, whose recent ancestors were inbreeding, and which is now becoming more outbred. Events. Taylor attended the following events: Invited Speaker, Department of Biology, Indiana University, February 2012; Invited Speaker, One Fungus - Which Name Symposium. Amsterdam, April 2012; Invited Speaker, University of Texas, Houston Medical Center, April 2012; Invited Speaker, IGERT Symposium, University of Arizona, Tucson, April 2012; Invited Speaker, Canadian Institute for Advanced Research Symposium, Quebec City, May 2012; Invited Speaker, ISHAM Triennial Congress, Berlin, June 2012; Invite Speaker, NIH-PSWRCE Meeting, Lake Tahoe, July 2012; Invited Speaker, A. Watson Armour Research Seminar, Field Museum, Chicago, September 2012 Services: Taylor served as an associate editor of Fungal Genetics and Biology; on the Editorial Boards of mBIO and IMAFungus; and as President of the International Mycological Association. Products: Taylor graduated: Students. none in 2012, Chris Ellison and Chris Villalta: one is currently in the lab. Postdocs. one in 2012, Prachand Shresthra; three are currently in the lab. Dissemination: See publications and our web site: http://plantbio.berkeley.edu/~taylor/ PARTICIPANTS: Individuals: Emily Whiston is a graduate student in Taylor's lab. Thomas Sharpton was a postdoc in Taylor's lab who is a now a postdoc at UCSF. G. Jui was an undergraduate in Taylor's lab who now is a graduate student at UCB. H.-Z. Wise and G. T. Cole are at the University of Texas, San Antonio. P. Corcoran and H. Johannesson are at the University of Uppsala. D. Jacobson and J. Kerekes were in or near Taylor's lab at UCB. P. Hickey and M. Bidartondo are in the UK. The partnerships are between Taylor and Johannesson at Uppsala and Taylor and Cole at UTSA. Whiston, Sharpton and Jui all received training that has propelled or is propelling them to the next stage in their academic careers. TARGET AUDIENCES: The target audiences are those working on microbial evolution and medical mycology. The effort is publishing sound and novel science. PROJECT MODIFICATIONS: There are no major changes in approach because we continue to let evidence of natural selection indicate genes of adaptive importance.

Impacts
A change in knowledge: We have identified the Coccidioides gene 509 as important to adaptation in this animal pathogenic fungus based on natural selection and based on elevated transcription in the pathogenic phase. If our hypothesis that this gene is important to pathogenicity is confirmed, the result could be important to preventing and treating coccidioidomycosis. We have found the first case of an inbreeding fungus that has begun to become more outbreeding. Given the far northern location of this population, where dogma suggests that it should be even more inbred, our finding may signal a change in thinking about fungal population biology. A change in actions: Having developed fungal comparative genomics, and having initiated fungal population genomics, we are moving toward genome wide association studies of wild populations of fungi with two new projects, one on Neurospora and one on thermophillic yeasts. A change in conditions: We have used two research systems, Neurospora and Coccidioides. Between them we have developed molecular phylogenetics, population genetics, phylogenomics and population genomics. Now, we are applying our knowledge to new species of Neurospora and to thermophillic yeasts, which should aid the effort to produce low-cost biofuels.

Publications

  • Whiston, E., Wise, H.-Z., Jui, G., Sharpton, T. J., Cole, G. T. and J. W. Taylor. 2012. Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp. PLoS One 7: e41034. PMID: 22911737
  • Corcoran, P., Jacobson, D. J., Bidartondo, M. I., Hickey, P. C., Kerekes, J. F., Taylor, J. W., and H. Johannesson. 2012. Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetrasperma. Fungal Biology 116:962-975. doi: 10.1016/j.funbio.2012.06.006. PMID:22954339


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: Activities. We used population genomics to identify genes responsible for adaptation to temperature and tested the hypotheses by gene deletion (Ellison et al. 2011). This is the first research to use population genomics to both discover populations and study their adaptation. We found loci that evolved by positive natural selection to enable female mate choice via postmating barriers in filamentous fungi (Turner et al. 2011). We used phylogenomics to discover the basis for intratetrad mating (homothallism) in Neurospora tetrasperma. We used evolved data and simulated data to test the utility of array-based competitive genome hybridization for phylogenetics (Gibert et al. 2011a, 2011b). We continued our research on gene duplication and gene family expansion in fungi (Muszweska et al. 2011). We published our first research on fungi that deconstruct plant cell walls in nature (Shrestha et al. 2011). We continued our longstanding efforts to simplify fungal nomenclature (Taylor 2011a, Hawskworth et al. 2011) and wrote two reviews that deal with recent advances in fungal biology (Roper et al. 2011, Taylor 2011b) Events. Taylor attended the following events: Invited Speaker, National University of Singapore, TLL, January 2011; Invited Speaker, Kasetser University, Bangkok, January 2011; Invited Speaker, California Native Plant Society, Marin Co. January 2011; Invited Speaker, Town and Gown, Berkeley, February 2011; Keynote Speaker, One fungus-One Name Symposium, Amsterdam, April 2011; Workshop Speaker, Human Pathogenic Fungi course, La Colle sur Loup, France, May 2011; Invited Speaker, Jacques Monod Conference on Emerging Fungal Disease, Roscof, France, June 2011; Keynote Speaker, European Congress of Mycology, Neos Marmaras, Greece, September 2011 Services: Taylor served as an associate editor of Fungal Genetics and Biology; on the Editorial Boards of mBIO and IMAFungus; and as President of the International Mycological Association. Products: Taylor graduated: Students. Two in 2011, Chris Ellison and Chris Villalta: one is currently in the lab. Postdocs. None in 2011, Four are currently in the lab. Dissemination: See publications and our web site: http://plantbio.berkeley.edu/~taylor/ PARTICIPANTS: One research specialist had the opportunity for career development: Tim Szaro, Research Specialist. One staff research assistant learned library preparation for next-generation sequencing: Flora Liu, Staff Research Assistant. Three postdocs learned about fungal evolution: Prachand Shrestha, Postdoc, Rachel Adams, Postdoc, Sara Branco, Postdoc. Three graduate students learned about fungal comparative genomics and fungal evolution: Chris Villalta, Graduate Student, Chris Ellison, Graduate Student, Emily Whiston, Graduate Student TARGET AUDIENCES: Target audiences include individuals, groups, market segments, or communities that were served by the project. Include population groups such as racial and ethnic minorities and those who are socially, economically, or educationally disadvantaged. Efforts include acts or processes that deliver science-based knowledge to people through formal or informal educational programs. Examples include: formal classroom instruction, laboratory instruction, or practicum experiences; development of curriculum or innovative teaching methodologies; internships; workshops; experiential learning opportunities; extension and outreach. Taylor target audience includes academics who study fungal evolution and pathogenic fungi. Included in his target audience are members of ethnic groups who are underrepresented in science, one of whom is a graduate student with Taylor. Efforts include teaching courses on microbial evolution and the biology of fungi and making scientific presentations at meetings. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
A change in knowledge: We found the most closely related fungal populations yet discovered and, in them, found regions of differentiation that contained genes involved in adaptation to latitude via temperature and day length (Ellison et al. 2011a). We followed up on our discovery of reinforced mating barriers by finding 10 loci that affect reinforcement by abortion of protoperithecia, the first report of reinforcement for fungi and the second for any type of postmating barrier (Turner et al. 2011). We found that three inversions account for the absence of recombination in the mating chromosome of a pseudohomothallic fungus, the first use of comparative genomics for this purpose (Ellison et al. 2011b). We showed that array genome hybridization is a poor way to do phylogenetics (Gilbert et al. 2011a, b). Our phylogenetics of proteases resulted in a reclassification of these enzymes and the discovery of many new groups of subtlisins (Muszewska et al. 2011). We made the first systematic search for fungi that deconstruct energy plant cell walls in nature and have brought 100 of the species into cultivation (Shrestha et al. 2011). Our efforts to bring fungal nomenclature into the 20th century, let alone the 21st century brought success, 20 years after our initial efforts (Taylor 2011, Hawksworth et al. 2011). A change in actions: Having developed fungal comparative genomics, we now initiated fungal population genomics, which allowed for the first genomic study of fungal adaptation. A change in conditions: We built on research on the pathogenic fungi, Coccidioides spp., by extending that research to the model fungus, Neurospora crassa. Here, we were able to test hypotheses about the role of specific genes in adaptation using gene disruption and tests of fitness. We now aim to use the lessons learned with Neurospora to inform our reseach on the pathogenic fungi.

Publications

  • Ellison, C. E., C. Hall, D. Kowbel, J. Welch, R. B. Brem, N. L. Glass, and J. W. Taylor. 2011. Population genomics and local adaptation in wild isolates of a model microbial eukaryote. PNAS 108:2831-2836.
  • Turner, E., Jacobson, D. J. and J. W. Taylor. 2011. Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection. PLoS Genetics 7:e1002204.
  • Ellison, C. E., Stajich, J. E., Jacobson D. J., Lapidus, A., Foster, B., Aerts. A., Riley, R., Lindquist, E. A., Grigoriev, I. V., and J. W. Taylor. 2011. Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. Genetics 189:55-69.
  • Gilbert, L. B., Kasuga, T., Glass, N. L., Taylor, J. W., 2011. Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees BMC Genomics. 12: Article Number: 487 DOI: 10.1186/1471-2164-12-487
  • Gilbert, L. B., Chae, L., Kasuga, T., Taylor, J. W., 2011. Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach. BMC Genomics. 12: Article Number: 456 DOI: 10.1186/1471-2164-12-456
  • Muszewska, A., Taylor, J. W., SzczÄ™sny, P. and M. Grynberg. 2011. Independent subtilases expansions in fungi associated with animals. Molecular Biology and Evolution 28: 3395-3404.
  • Shrestha, P., Szaro, T. M., Bruns, T. D., and J. W. Taylor. 2011. Systematic search for cultivatable fungi that best deconstruct cell walls of Miscanthus and sugarcane in the field. Applied and Environmental Microbiology 77:5490-5504.
  • Taylor, J. W., 2011. One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2:113-120.
  • Hawksworth, D. L., Crous, P. W., Redhead, S. A., Reynolds, D. R., Samson, R. A., Seifert, K. A., Taylor, J. W., Wingfield, M. J., et al. 2011. The Amserdam declaration on fungal nomenclature. IMA Fungus. 2:105-112.
  • Roper, M., Ellison, C., Taylor, J., and N. L. Glass. 2011. Nuclear and genome dynamics in multinucleate ascomycete fungi. Current Biology 21:R786-793.
  • Taylor, J.W. 2011. Keynote paper: The poetry of mycological accomplishment and challenge. Fungal Biological Reviews 25:3-13.


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: Activities. We used new Bayesian phylogenetic methods to assess the dating of deep divergences in fungal evolution (Berbee and Taylor 2010). We conducted one fo the first population genomic studies of fungi and found that introgression between species may be driven by positive selection for genes in the introgressed region (Neafsey et al. 2010). We documented the first example of reinforcement of reproductive barriers in fungi (Turner et al. 2010). We also commented on genomics of complex fungi, that is mushrooms (Taylor and Ellison 2010) and the need to document new species (Hawksworth et al. 2010). In the lab, we continue to compare transcrptomes of Coccidioides species and genomes of Coccidioides with those of close neighbors with the aim of understanding what makes Coccidioides species such powerful pathogens. We also continue to compare genomes of Neurospora individuals for population genomic studies of the early events in speciation. Taylor mentored two postdocs and three students. He taught a graduate course (PMB 220c) on microbial evolution and two undergraduate courses on mycology (PMB 110/110L). Events.Taylor attended the following events: Invited Speaker, Canadian Inst. for Advanced Study, UBC, Vancouver, January 2010; Keynote Speaker, Fungal Dimorphic Pathogens, ASM, Miami, March 2010; Invited Speaker, European Neurospora Conference, Leiden, March 2010; Plenary Speaker, European Fungal Genetics Conference, Amsterdam, March 2010; Invited Speaker, National University of Singapore, TLL, May 2010; Keynote Speaker, International Mycological Congress IX, Edinburgh, August 2010 Service: Taylor served as an associate editor of Fungal Genetics and Biology; on the Editorial Boards of mBIO and IMAFungus; and as President of the International Mycological Association. Products: Taylor graduated: Students. None in 2010, three are currently in the lab. Postdocs. None in 2010, two are currently in the lab. Dissemination: See publications and our web site: http://plantbio.berkeley.edu/~taylor/ PARTICIPANTS: One research specialist had the opportunity for career development: Tim Szaro, Research Specialist. One staff research assistant learned library preparation for next-generation sequencing: Flora Liu, Staff Research Assistant. Two postdocs learned about fungal evolution: Prachand Shrestha, Postdoc and Elizabeth Turner, Postdoc. Three graduate students learned about fungal comparative genomics and fungal evolution: Chris Villalta, Graduate Student, Chris Ellison, Graduate Student, Emily Whiston, Graduate Student TARGET AUDIENCES: Taylor target audience includes academics who study fungal evolution and pathogenic fungi. Included in his target audience are members of ethnic groups who are underrepresented in science, one of whom is a graduate student with Taylor. Efforts include teaching courses on microbial evolution and the biology of fungi and making scientific presentations at meetings. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
A change in knowledge: We found that well diverged fungal species can exchange genes, as much as 7% of their genomes, through introgression (Neafsey et al. 2010). In one introgressed region, we found a gene known to influence virulence in the pathogenic fungi, Coccidioides immitis and C. posadasii. Now, we have data that other genes in the introgressed region may be important to pathogenicity. We reported on the first case of reinforced barriers to sexual reproduction in fungi (Turner et al. 2010). These barriers are known from animals, but had not been seen in fungi. We also found that the barrier was a postmating barrier, which is very rare in animals but may be common in fungi. Our work also documents the first case of female mate choice in a microbe, albeit the choice is among speices and not individuals in a species. Our study of the "molecular clock" of phylogenetics established that different fungal lineages evolve at different rates and that calibration of the tree using fossils has the largest effect on the dates assigned to divergences throughout the tree (Berbee and Taylor 2010). Our study casts doubt on studies supporting the divergence of fungi and animals at earlier than 1.5 billion years ago and argues for a divergence closer to 1 billion years ago. Our study also calls into question the assignment of a well preserved, 400 million year old fossil to the Pyrenomycetes rather than a much earlier diverging group. A change in actions: Since 2008 we have been developing comparitive genomics, comparative transcriptomics and population genomics using next-generation sequencing. Although the switch has been time consuming, the new action will improve the quality and quantity of our data and help us meet our goals for the coming years. A change in conditions: Again this year, our principal change of condition concerns the evolution of pathogenic fungi. This year we discovered that what we had considered to be genetically isolated species were capable of exchanging genes via introgression at a significant rate, 7% between two species that have been diverged for ca. 5 million years. Because selection for genes in the introgressed regions must be involved in their spread, we have found another means of indentifying genes that may be important to pathogenicity in fungal pathogens.

Publications

  • Hawksworth, D. L., Cooper, J. A., Crous, P. W., Hyde, K. D., Iturriaga, T., Kirk, P. M., Lumbsch, H. T., May, T. W., Minter, D. W., Misra, J. K., Norvell, L., Redhead, S. A., Rossman, A. Y., Seifert, K. A., Stalpers, J. A., Taylor, J. W., Wingfield, M. J. 2010. Proposals 117-119: To make the pre-publication deposit of key nomenclatural information in a recognized repository a requirement for valid publication of organisms treated as fungi under the CODE. Mycotaxon. 111: 514-519.
  • Neafsey, D. E., Barker, B. M., Sharpton, T. J., Stajich, J. E., Park, D. J., Whiston, E., Hung, C. Y., McMahan, C., White, J., Sykes, S., Heiman, D., Young, S., Zeng, Q. D., Abouelleil, A., Aftuck, L., Bessette, D., Brown, A., FitzGerald, M., Lui, A., Macdonald, J. P., Priest, M., Orbach, M. J., Galgiani, J. N., Kirkland, T. N., Cole, G. T., Birren, B. W., Henn, M. R., Taylor, J. W., Rounsley, S. D., 2010. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research. 20: 938-946.
  • Berbee, M. L. and Taylor, J. W. 2010. Dating the molecular clock in fungi -- how close are we Fungal Biology Reviews 24:1-16.
  • Taylor, J. W. and C. E. Ellison. 2010. Mushrooms: Morphological complexity in the fungi. Proceedings of the National Academy of Sciences (USA) 107: 11655-11656.
  • Turner, E., D. J. Jacobson, et al. 2010. Reinforced postmating reproductive isolation barriers in Neurospora, an Ascomycete microfungus. Journal of Evolutionary Biology 23: 1642-1656.


Progress 10/01/09 to 12/31/09

Outputs
OUTPUTS: Outputs. Activities. We compared genomes of Coccidioides species, which are pathogens, and related fungi to study fungal genome evolution. We assembled collections of Lacazia loboi isolates to assess the genetic independence of this group of pathogenic fungi. genetically isolated clades in this species. We applied population genetics methods to the amphibian pathogen, Batrachochytrium dendrobatidis, to understand the origin of the epidemic. We described three new species in the model eukaryote, Neurospora. We summarized fungi for Current Biology. Taylor mentored two postdocs and three students. He taught a graduate course (PMB 220c) on microbial evolution and two undergraduate courses on mycology (PMB 102/102L). Events.Taylor attended the following events: Invited Speaker, Duke University Medical School, April 2009; Invited Speaker, FEBS Advanced Course on Human Fungal Pathogen, La Colle-sur-Loup, France, May 2009; Invited Speaker, Swiss Evolution Workshop, La Fouley, Switzerland, June 2009; Invited Speaker, Evolution and Medicine, University of Toulouse, October 2009. Services: Taylor served as an associate editor of Fungal Genetics and Biology; as Vice-President of the International Mycological Association. Products: Taylor graduated: Students: Dr. Thomas Sharpton, Postdoc, Gladstone Inst. UCSF, San Francisco; Dr. Elizabeth Turner Postdoc, PMB, UCB, Berkeley. Dissemination: See publications and our web site: http://plantbio.berkeley.edu/~taylor/ PARTICIPANTS: One research specialist had the opportunity for career development: Tim Szaro, Research Specialist. One staff research assistant learned library preparation for next-generation sequencing: Flora Liu, Staff Research Assistant. Two postdocs learned about fungal evolution: Prachand Shrestha, Postdoc and Elizabeth Turner, Postdoc. Three graduate students learned about fungal comparative genomics and fungal evolution: Chris Villalta, Graduate Student, Chris Ellison, Graduate Student, Emily Whiston, Graduate Student TARGET AUDIENCES: Our target audience is scientists conducting research on fungi, including those working with agriculturally important plant pathogenic fungi. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Outcomes/Impacts. A change in knowledge: We found that gene family expansion in proteases accompanied the shift from plant based nutrition to animal based nutrition in Coccidioides species (Sharpton et al. 2009) and that gene family contraction in proteins that can attack plant cell walls accompanied the same change. In the same study, we also showed that significant positive selection helped form the genomes of the pathogens, Coccidioides immitis and C. posadasii. We used genome sequence to show that the chytridiomycosis is due to a recent spread of the fungal pathogen (James et al. 2009). We showed that Lacazia is a close relative of Histoplasma (Vilela et al. 2009). We described three new Neurospora species (Villalata et al. 2009). A change in actions: We have spent the past two year shifting to comparitive genomics and comparative transcriptomics using next-generation sequencing. Although the switch continues to be time consuming, the new action will improve the quality and quantity of our data and help us meet our goals for the coming years. A change in conditions: Our principal change of condition concerns the evolution of pathogenic fungi. We have shown that pathogenic fungal species must be characterized by genetic means because different genetic species have different attributes that include virulence and toxins. Lumping taxa by phenotype will confound attempts to prevent or to remedy these diseases. We have begun to use the knowledge of genetically isolated species to detect the action of selection on specific genes, which then become candidates for virulence factors.

Publications

  • Stajich, J. E., Berbee, M. L., Blackwell, M., Hibbett, D. S., James, T. Y., Spatafora, J. W., Taylor, J. W. 2009. The Fungi. Current Biology 19: R840-845.
  • James, T. Y., Litvintseva, A. P., Vilgalys, R., Morgan, J. A. T, Taylor, J. W., Fisher, M. C., Berger, L., Weldon, C., du Preez, L., Longcore, J. E. 2009. Rapid Global Expansion of the Fungal Disease Chytridiomycosis into Declining and Healthy Amphibian Populations. PLoS Pathogens 5: e1000458.
  • Sharpton, T. J., Stajich, J. E., Rounsley, S. D., Gardner, M. J., Wortman, J. R., Jordar, V. S., Maiti, R., Kodira, C. D., Neafsey, D. E., Zeng, Q., Hung, C.-Y., McMahan, C., Muszewska, A., Grynberg, M., Mandel, M. A., Kellner, E. M., Barker, B. M., Galgiani, J. N., Orbach, M. J., Kirkland, T. N., Cole, G. T., Henn, M. R., Birren, B. W., and Taylor, J. W. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research 19 1722-1731.
  • Villalta, C. F., Jacobson, D. J., Taylor, J. W. 2009. Three new phylogenetic and biological Neurospora species: N. hispaniola, N. metzenbergii and N. perkinsii. Mycologia 101: 777-789.
  • Vilela, R., Rosa, P. S, Belone, A. F. F, Taylor, J. W., Diorio, S. M., Mendoza, L. 2009. Molecular phylogeny of animal pathogen Lacazia loboi inferred from rDNA and DNA coding sequences. Mycological Research 113: 851-857.